Front Cover 1
Biogeochemistry of Inland Waters 4
Copyright Page 5
Editor 6
Contributors 8
Contents 12
Introduction to the Biogeochemistry of Inland Waters 16
References Cited/Further Reading 17
Properties of Water 18
Chemical Properties of Water 18
Introduction 18
The Structure of Water 18
Solvation by Water 20
The Reactivity of Water 23
Trends and Patterns in Limnology 23
Dissolved Gases 23
Major Ions 24
Nutrients 24
Conclusion 25
Further Reading 25
Relevant Websites 26
Physical Properties of Water 27
Introduction 27
Density 27
Heat Capacity/Specific Heat 28
Heat of Fusion/Melting 29
Heat of Vaporization/Condensation 30
Isotopes 30
Sublimation 31
Surface Tension and Cohesiveness 31
Viscosity 32
Colligative Properties 32
Further Reading 32
Pressure 34
Introduction 34
Hydrostatic Pressure 34
Density Variations 37
Hydrostatic Forces on Submerged Surfaces 37
Buoyancy 39
Dynamic Pressure 40
Pressure in the Equations of Motion 41
Biological Responses 42
Further Reading 43
Relevant Websites 44
Gas Exchange at the Air-Water Interface 45
Introduction 45
Basic Gas Exchange Principles 45
Physical Factors 45
Mechanistic Models of Gas Transfer 46
Chemical Factors 47
Solubility of Gases 48
Diffusion Coefficient 48
Chemical Enhancement 48
Other Factors 49
Meteorological Conditions 49
Surfactants 49
Bubbles 49
Methods for Estimating Gas Exchange Rates 50
Purposefully Released Tracers 50
Chambers and Enclosures 50
Eddy Correlation Methods 50
Empirical Models of Gas Exchange 51
Other Important Aspects of Gas Exchange 52
Conclusion 52
Further Reading 53
Light, Photolytic Reactivity and Chemical Products 54
Photochemistry Starts from the Absorption of Solar Radiation 54
Primary Photophysics and Subsequent Secondary Chemical Reactions 54
Photochemistry of Organic Carbon 54
Photochemistry of Nitrogen 57
Photochemistry of Phosphorus 57
Coupling of Photooxidation of Organic Matter to the Photoreduction of Metals 57
Heterogeneous Photochemistry 57
Photochemical Reactivity of Organic Matter 58
Regulators of the Photochemical Reactivity of Organic Matter 59
Predicting the Rates of Photoreactions in the Environment 60
Solar Radiation Spectrum Responsible for Photochemical Reactions 62
Rates of Photochemical Reactions in the Environment 62
Responses of Food Webs to the Photochemical Transformation of Organic Matter 62
Contribution of Photochemistry to the Biogeochemistry of Organic Matter 64
Further Reading 65
Hydrology 68
Hydrological Cycle and Water Budgets 68
Introduction 68
Hydrological Cycle 68
Hydrological Cycle: Lithospheric Components 70
Surface water 70
Soil water 70
Ground water 70
Nutrient Cycling and Energy Balance 71
Summary 72
Water Budgets 72
Framework 72
Assessment of Components 72
Evapotranspiration 72
Soil-water storage 73
Groundwater storage 73
Groundwater runoff 73
Two Examples 74
Global water balance 74
California 74
Epilogue 74
Further Reading 74
Atmospheric Water and Precipitation 75
Introduction 75
Precipitation Formation 76
Water Vapor in the Atmosphere 76
Cloud Formation 77
From Cloud Particles to Precipitation 77
Precipitation Observations 78
Rain Gauges 78
Radar 78
Satellite Remote Sensing 79
Modeling Precipitation 81
Scale-Invariant Statistical Models 81
Conclusions 83
Glossary 83
Further Reading 84
Relevant Websites 84
Snow and Ice 85
Further Reading 85
Relevant Websites 85
Evapotranspiration 86
Introduction 86
Evaporation and the Projected Acceleration in the Global Hydrologic Cycle 86
Evapotranspiration and the Continental-Scale Hydrologic Cycle 87
Evapotranspiration at Local Scales: Knowledge Gaps and Why the Problem of its Quantification Persists 90
Conclusions 92
Further Reading 92
Vadose Water 93
Introduction 93
Fundamental Processes of Vadose Water 93
Unsaturated Hydrostatics 93
Water content 93
Water pressure and energy 93
Water retention 94
Examples 95
Practical significance 96
Measurement or estimation of water retention 96
Empirical formulas for water retention 96
Diffuse Unsaturated Flow 96
Darcy's law for vadose water 97
Unsteady diffuse flow 97
Unsaturated hydraulic conductivity 97
Measurement or estimation of unsaturated K 97
Empirical formulas for unsaturated K 98
Effects of dissimilar materials 98
Preferential Flow 98
Types of preferential flow 98
Quantification of preferential flow 99
Vadose Water in the Hydrologic Cycle 100
Moisture State in the Vadose Zone 100
Moisture Dynamics in the Vadose Zone 101
Interactions at the land surface 101
Infiltration 101
Evapotranspiration 101
Redistribution of infiltrated water 102
Aquifer Recharge 103
Conclusion 103
Further Reading 104
Ground Water 105
Introduction 105
Aquifer Basics 105
Groundwater Flow Systems 106
Recharge 107
Groundwater Budgets 107
Effects of Pumping on Groundwater Budgets 108
Effects of Climate on Groundwater Budgets 108
Groundwater Quality 109
Groundwater Data and Models 109
Further Reading 110
Relevant Websites 111
Ground Water and Surface Water Interaction 112
Introduction 112
SW-GW Interaction: Scales and Effects 112
Measuring GW-SW Interaction: Methods and Approaches 112
Direct Measures of Exchange 113
Heat Tracer Methods 113
Use of Darcy's Law 113
Mass-Balance Approaches 114
GW-SW Interactions across the Inland Hydrosphere 116
Streams 116
The Hyporheic Zone and Transient Storage Modeling 117
Rivers and Floodplains 118
Lakes and Wetlands 120
Human Impacts and Future Research 121
Agricultural Development 121
Urbanization 122
Hydrosphere Modifications 122
Future Research 122
Glossary 122
Further Reading 122
Relevant Websites 123
Groundwater Chemistry 124
Introduction 124
Chemical Composition Changes along Groundwater Flow Paths 124
Chemical Composition Changes in Ground Water due to Human Activity 128
Geochemical Models and Mass Balance Examination of Chemical Composition Changes in Ground Water 133
The Relation of Chemical Characteristics of Ground Water to Chemical Characteristics of Surface Water 133
Further Reading 134
Relevant Websites 134
Fluvial Export 135
Riverine Fluxes and Earth System 135
River Data Bases 135
Riverine Fluxes at Stations 136
Daily to Seasonal Variations of Riverine Fluxes at Stations 136
Flux Determination from Discrete Sampling 136
Flux Durations 137
Interannual Variations of Fluxes 137
Geographic Variability of Riverine Fluxes 137
Particulate Fluxes and TSS Levels 137
Major Ions and Total Dissolved Solids 141
Major World Rivers and Their Ranked Fluxes 141
Human Impacts on Riverine Fluxes 144
Total Suspended Solids and Total Dissolved Solids 144
Nutrients in World Rivers: From Natural to Contemporary Loads 144
Nutrients Trends and Changes in Stoechiometric N: P:Si Ratios 145
Trajectories of Riverine Fluxes Reflect Pressures Evolution and Water Quality Management 145
Further Reading 146
Relevant Websites 147
Fluvial Transport of Suspended Solids 148
Introduction 148
Equilibrium Transport of Sediment Suspensions 148
Nonequilibrium Transport of Sediment Suspensions 149
Further Reading 150
Streams 151
Introduction 151
Spatial Organization of Streams in Drainage Networks 151
Sources of Flow in Streams 152
Movement of Water into Stream Channels 153
Movement of Sediment into Stream Channels 155
Characteristics of Flow in Streams 156
Glossary 158
Further Reading 159
Relevant Websites 159
Rivers 160
What is a River? 160
Hydrology and Geomorphology 160
Water Sources and Discharge 160
Flooding 161
Water Movement 162
Geomorphology 163
Water Regulation 164
Water Quality 165
Particulate Matter 165
Dissolved Substances 165
Nutrients 166
Dissolved Gases 166
Pollutants 167
Biology of Rivers 167
Primary Producers 167
Invertebrates 168
Fishes 169
River Food Webs 169
Global Biogeochemical Cycling 170
Glossary 171
Further Reading 171
Springs 172
What are Springs? 172
Geological Origin of Springs 172
Kinds of Springs 172
Biology of Springs 174
Nonthermal Springs 174
Thermal Springs 182
Importance of Springs 184
Geological Importance 184
Ecological Importance 185
Scientific Importance 185
Cultural and Societal Importance 189
Conservation of Springs 190
Glossary 191
Further Reading 192
Relevant Websites 192
Wetland Hydrology 194
Introduction 194
Water Sources 194
Factors Contributing to Wetland Hydrology 194
How Wet is a Wetland? 196
Wetland Hydrology Defined 196
Depth of Saturation 196
Duration of Wetness 196
Frequency of Prolonged Wetness 196
Growing Season 197
Does Prolonged Saturation Guarantee Anaerobic and Reducing Conditions? 197
Wetland Water Regimes 198
Hydrographs for Different Wetland Types 198
Changing Water Levels 199
Water Budget 199
Inputs 200
Outputs 202
Annual Water Budgets 202
Wetland Hydrology Indicators 202
Glossary 204
Further Reading 205
Relevant Websites 205
Hydrodynamics and Mixing in Lakes, Reservoirs, Wetlands and Rivers 206
Biological-Physical Interactions 206
Introduction 206
Water Movements - The Concept of Scale 206
Small-Scale Turbulence 207
Physical Influences on the Size and Structure of Organisms 208
Turbulent Extent and the Pelagic Habitat 209
Mixed Layer Depth and the Maintenance of Non-motile Plankton 209
Physical Influences on Nutrient Fluxes 210
Nutrient Fluxes at the Microscale 210
Further Reading 212
Density Stratification and Stability 213
Introduction 213
Circulation Patterns 213
Density Differences and Formation of Layers 214
Temperature Stratification 214
Thermobaric Stratification 215
Salinity Stratification 216
Processes Forming Gradients of Dissolved Substances 217
Episodic Partial Deep Water Renewal 218
Quantifying Stability 218
Temperature 218
Salinity, Electrical Conductivity and Electrical Conductance 218
Density 219
Stability 219
Differential Quantities 220
Bulk Quantities 221
Nomenclature 218
Further Reading 222
Relevant Websites 223
The Surface Mixed Layer in Lakes and Reservoirs 224
Background 224
Mixed Layer Motions and Turbulence 224
Basic Ideas of Turbulence (refer 'see also' section) 224
Winds on Lakes 225
Surface Energy Exchanges 228
Mixed Layer Deepening and Entrainment 230
Mixing and Turbulence Energetics 230
Upwelling 233
Synthesis 234
Summary 238
Further Reading 238
Small-Scale Turbulence and Mixing: Energy Fluxes in Stratified Lakes 239
Introduction 239
Density Stratification and Mixing - the Basin Scale 239
Density Stratification and Mixing - the Small Scale 239
Density Stratification and Mixing - the Turbulent Transport 242
Turbulence and Mixing in Stratified Lakes and Reservoirs 242
Turbulence Production in the Surface and Bottom Boundaries 242
Internal Waves and Turbulence in the Stratified Interior 244
Turbulent Energy Flux through the Water Column - Synthesis 245
Further Reading 246
The Benthic Boundary Layer (in Rivers, Lakes, and Reservoirs) 247
Introduction 247
Definition and Relevance of the Benthic Boundary Layer 247
Structure of the BBL 247
The Transport of Momentum 247
The Turbulent BBL 247
The Viscous Sublayer 249
Effects of Bottom Roughness 249
Oscillatory Boundary Layers 250
Stratified BBL 250
Effects of Density Stratification 250
2-Dimensional Mixing Processes in Enclosed Basins 250
Turbulence Induced by Internal Wave Interactions with Bottom Boundaries 251
Solute Transport and Sediment-Water Exchange 251
The Diffusive Sublayer 251
Effects of Small-Scale Sediment Topography 253
Nondiffusive Fluxes 254
In Situ Flux Measurements 254
Particle Dynamics 254
Glossary 255
Further Reading 255
Currents in Rivers 256
Introduction 256
Controlling Factors and Classifications of Currents 256
Currents in Fluvial Channels 257
Secondary Currents 258
Structure of Currents at River Confluences 259
Currents at Engineering Structures 260
Navigation-Induced Currents 261
Nomenclature 262
Further Reading 263
Relevant Websites 263
Currents in Stratified Water Bodies 1: Density-Driven Flows 264
Introduction 264
Characteristics of Density Currents 264
Density Plumes Generated by External Inputs 266
River Inflows 266
Interbasin Exchange 267
Subsurface Inflows 268
Density Plumes Generated by Internal Processes 268
Differential Cooling 268
Thermal Bar 268
Thermal Baricity 270
Turbidity Currents Generated by Waves 271
Horizontal Density Currents Generated under Ice Cover 271
Density Currents in Tropical and Saline Lakes 271
Impact of Changes in the Environmental Conditions on Density Currents and Deep-Water Renewal 271
Further Reading 272
Currents in Stratified Water Bodies 2: Internal Waves 273
Introduction 273
Characteristic Geometry and Water-.Column Stratification 273
Surface Momentum Transfer and Wind Set-Up 273
Wind Set-Up of the Free Surface 273
Wind Set-Up of the Internal Stratification 274
Wedderburn and Lake Numbers 276
Basin-Scale Standing Wave Motions (Seiches) 277
Interfacial Waves in a Layered Stratification 277
Horizontal modes 277
Vertical modes 279
Internal Modes in a Continuous Stratification 280
Degeneration of Basin-Scale Internal Waves in Lakes 281
Regime 1: Damped Linear Waves 282
Regime 4: Kelvin-Helmholtz Billows 282
Regime 3: Supercritical Flow 284
Regime 2: Solitary Waves 284
Shoaling of Nonlinear Internal Waves 285
Progressive Internal Wave Rays in a Continuous Stratification 286
Resonant and Forced Internal Waves 288
Analysis of Timeseries Data 288
Summary 291
Further Reading 292
Currents in Stratified Water Bodies 3: Effects of Rotation 294
Introduction 294
Governing Equations 295
Gravity Waves 295
Current Structure and Measurement 299
Vorticity Waves 300
Practical Guide to Measurement of these Waves 301
Nomenclature 301
Glossary 302
Further Reading 302
Currents in the Upper Mixed Layer and in Unstratified Water Bodies 303
Introduction 303
Fundamental Concepts 304
Shallow Water Equations 304
Lateral and Vertical Circulations 304
Rotational Effects in Shallow Layers 305
Wind Setup 305
Lateral Circulation 306
Generation of Circulation in Homogenous Layers 306
Topographic Gyres in Homogenous Basins 306
Topographic Waves in Homogenous Bodies 307
Spatial Variability of Wind Forcing 309
Other Sources of Circulation 310
Vertical Circulation 310
Circulation Patterns in Natural Systems (Lakes and Reservoirs) 314
Conclusions and Future Research Needs 316
Further Reading 316
Flow in Wetlands and Macrophyte Beds 318
Lakes 318
Nontidal Wetlands 323
Rivers 324
Saltmarshes and Mangroves 327
Summary 327
Nomenclature 327
Further Reading 329
Relevant Websites 329
Flow Modification by Submerged Vegetation 330
Introduction 330
Distribution of Flow in and above the Vegetation 330
Turbulence Structure with Submerged Canopies 332
Sparse and Dense Canopies 333
Flexible Canopies 333
Canopy Water Renewal 333
Summary 335
Further Reading 336
Hydrodynamical Modeling 337
Introduction 337
Dimensionality and Capabilities 337
Boundary and Initial Conditions 339
Calibration 341
Hydrostatic Approximation 341
Model Grid 341
Overview 341
Grid Size and Convergence 344
Horizontal Grid Systems 344
Vertical Grid Systems 346
Time Step 347
Numerical Methods 347
Order of Accuracy 348
Model Errors 348
Modeling Turbulence and Mixing 348
Similarities and Differences between Lake and River Modeling 349
Summary and Future Directions 349
Further Reading 351
Inorganic Chemicals: Cycles and Ecosystem Dynamics 352
Chemical Fluxes and Dynamics in River and Stream Ecosystems 352
Introduction 352
Transport 354
Oxic Processes 356
Anoxic Processes 357
Overview 358
Glossary 358
Further Reading 359
Dissolved CO2 360
The Dissolve Inorganic Carbon System 360
Dissolved CO2 - A Master Variable 360
Atmospheric Exchange of CO2 361
Regulation of Dissolved CO2 in Aquatic Ecosystems 362
Regulation of pH by Dissolved CO2 362
Measurement and Calculation of Dissolved CO2 363
Measurement 363
Calculation 364
Glossary 364
Further Reading 364
Glossary 364
Alkalinity 365
Introduction 365
Chemistry of Buffers 365
Chemical Background 365
Measurement 365
Effect of Carbon Dioxide 366
Origin of Alkalinity 367
Weathering 367
Cation Exchange 367
Assimilatory Uptake 367
Dissimilatory Redox Reactions 367
Evaporation and Precipitation 368
Biology of Alkaline and Acidic Lakes 368
Natural Buffering 368
Low Alkalinity Acidic Waters 369
Highly Alkaline Lakes 370
Further Reading 370
Relevant Websites 370
Major Cations (Ca, Mg, Na, K, Al) 371
Cation Functions and Stoichiometry 371
Sources of Major Cations 371
Biological and Geochemical Sinks for Major Cations 372
Analytical Distinctions among Cations 373
Cation Chemistry in Fresh Waters 373
Environmental and Anthropogenic Influences on Cation Chemistry 376
Nomenclature 376
Further Reading 377
Relevant Websites 377
Chloride 378
Introduction: Chloride and Salinization 378
Natural and Anthropogenic Sources of Chloride to Inland Waters 378
Ecological Implications of Increased Chloride Concentrations 381
Retention of Chloride within Watersheds and Inland Waters 382
Conclusions 382
Knowledge Gaps 382
Further Reading 383
Relevant Websites 384
Iron and Manganese 385
Introduction 385
Iron and Manganese Chemistry 385
Redox Reactions 385
Major Chemical Forms in Natural Waters 385
Chemical Interactions through Adsorption onto Fe and Mn Oxides 386
Fe and Mn in Rivers and Streams 386
The World's Major Rivers 386
Smaller Streams and Rivers 387
Fe and Mn in Lakes 388
Inputs 388
Losses 388
Cycling within Sediments 388
Lakes 388
Streams and Rivers 390
Cycling within the Water Column 390
Lakes 390
Streams and Rivers 391
Fe and Mn Oxides and Trace Metals 391
Special Environments 392
Waters Receiving Acid Mine Drainage or Acid Rock Drainage 392
Hydrothermally Influenced Water Bodies 393
Glossary 394
Further Reading 394
Micronutrient Elements (Co, Mo, Mn, Zn, Cu) 395
Introduction 395
Cobalt 395
Molybdenum 396
Manganese 397
Zinc 397
Copper 398
Conclusion 398
Glossary 398
Further Reading 399
Glossary 399
Biogeochemistry of Trace Metals and Mettaloids 400
Introduction 400
Essential and Nonessential Trace Elements 400
Sources of Trace Elements 400
Geological Sources 400
Anthropogenic Sources 401
Point source pollution 401
Nonpoint source pollution 401
Sources to the atmosphere 401
Biogeochemistry of Trace Metals in Fresh Waters 401
Aqueous Complexation 402
Phase Partitioning 403
Oxidation, Reduction, and Speciation 403
Microbial Metal Reduction and Oxidation 404
Biological Uptake, Accumulation, and Transformation of Metals 404
Metal Resistance Mechanisms 405
Example: Arsenic and Selenium 405
Example: Mercury 405
MeHg Production 406
MeHg Demethylation and Hg Reduction 407
Temporal and Spatial Controls on Net Hg Methylation 407
MeHg Accumulation in Food Webs 407
Solving the Mercury Problem 407
Further Reading 408
Relevant Websites 408
Nitrogen Fixation 409
Introduction to Biological Nitrogen Fixation in Aquatic Systems 409
Nitrogen Fixation by Heterotrophic Bacteria in Sediments 410
Nitrogen Fixation by Planktonic Cyanobacteria in Freshwater Lakes 410
Nitrogen Fixation by Planktonic Cyanobacteria in Saline Waters 413
Nitrogen Fixation by Benthic and Epiphytic Cyanobacteria 414
Conclusions 414
Glossary 415
Further Reading 416
Glossary 416
Nitrogen 417
Introduction 417
Forms and Transformations of Nitrogen 417
Nitrogen Cycling at the Ecosystem Scale 419
Nutrient Limitation of Net Primary Production 420
Human Acceleration of the Nitrogen Cycle 421
Glossary 423
Further Reading 423
Phosphorus 425
Introduction 425
History of P Research and Basic Chemical Properties of P 425
P Limitation of Production in Inland Waters 426
Global Regional and Landscape Transfers of P 427
P Cycling and Retention in Inland Waters 428
Continuing Research on the P Cycle 430
Glossary 430
Further Reading 430
Silica 431
Si Cycling at the Ecosystem Scale 431
Silica Cycling in Natural Waters 432
DSi Limitation 432
Human Influence on Si Cycling 433
Continuing Research on the Si Cycle 434
Glossary 434
Further Reading 434
Salinity 435
Ecological Responses 436
Salt as a Conservative Tracer in Watersheds 437
Dryland Salinity and Salinization of Inland Waters 438
Further Reading 439
Organic Compounds: Cycles and Dynamics 442
Allelochemical Reactions 442
Introduction 442
Terminology 442
Experimental Approaches Studying Allelochemical Reactions 443
Range of Allelochemical Reactions 443
Animal-Animal Interactions 444
Fish Kairomones 444
Invertebrate Kairomones 445
Alarm Cues 446
Partner Finding and Kin Recognition 446
Plant-Animal Interactions 446
Impact of Plants on Grazing and Herbivory 446
Cyanobacterial toxins 446
Herbivore deterrents 448
Foraging kairomones 449
Impact of Grazers on Plants 449
Plant-Plant Interactions 449
Allelopathy 449
Autotoxicity 452
Algal Pheromones 452
Allelochemical Reactions Involving Heterotrophic Microorganisms 453
Further Reading 453
Carbohydrates 454
Introduction 454
Carbohydrates and their Building Blocks 454
Carbohydrates in Aquatic Environments 454
Analytical Problems Measuring Carbohydrates in Natural Waters 454
Colorimetric Methods 454
Chromatographic Methods 456
Comparison of Methods 456
Concentrations of Dissolved Free and Combined Carbohydrates 456
Total Amounts of Carbohydrates 456
Carbohydrates Relative to DOC 456
Free Monosaccharides 456
Sources of Carbohydrates in Water 459
Release by Phytoplankton 459
Release by Colony-Forming Algae and Plants 459
Other Sources of Carbohydrates 459
Composition of Carbohydrates in Water 459
Carbohydrates in Algae and Dissolved in Water 459
Natural Saccharides in Fresh Water 459
Dynamic Concentrations of Dissolved Carbohydrates 460
Annual Variations in Carbohydrate Pools 460
Daily Variations in Carbohydrate Pools 461
Carbohydrates and Algae in Running Waters 462
Relations Between Carbohydrates and Phytoplankton in a Large Lake 462
Assimilation of Carbohydrates 462
Uptake of Carbohydrates and Bacterial Growth 462
Uptake of Glucose and Fructose 462
Measurements of Uptake of Free Saccharides 464
Uptake of all Carbohydrates and Bacterial Growth 464
Utilization of Polysaccharides Requires Enzymes 464
Enzymatic Activity in a French River Reservoir 466
Special Polysaccharides: TEP and Alginates 467
Transparent Exopolymer Particles 467
Alginates 467
Carbohydrates in Humic Matter 467
Carbohydrates and Stable Isotopes 467
Application of Stable Isotopes in Ecology 467
Tracing of Carbohydrates in a Food Web 468
Carbohydrates - From Molecule to Trees 468
Further Reading 469
Carbon, Unifying Currency 470
Introduction 470
Carbon Pools 470
A Simplified Carbon Cycle for Inland Waters 470
The Predictability of Carbon-Based Aquatic Processes 472
Patterns of Organic Matter Production 472
Patterns of Organic Matter Oxidation 472
Glossary 473
Further Reading 473
Dissolved Humic Substances: Interactions with Organisms 474
Introduction 474
Interference within Photosynthetic Oxygen Production 474
Hormone-Like Effects 475
Chemical Attraction and Gene Regulation in C elegans 475
Interaction with Membranes 476
Chemical Stress Defense 477
Acquisition of Multiple Stress Resistance 478
Conclusion 479
Glossary 479
Further Reading 480
Interactions of Dissolved Organic Matter and Humic Substances 481
Introduction 481
The Physical Appearance of Humic Substances in Water 481
Colloidal Organic Matter 483
Aggregation 483
Mechanisms of Collisions and Formation of Colloids and Larger Particles 484
Size and Concentration 484
Brownian Motion (Thermal Effects) 484
Shear (Flow Effect) and Turbulence 485
Differential Settling (Gravity Effects) 485
Diffusive Capture 485
Surface Coagulation and Bubbling 485
Filtration 485
Microbial Activity and TEP 485
Cations, pH, and Adsorption to Particles 485
Sunlight 485
The Role of Iron for Aggregation 485
Interactions of DOM and Humic Substances with Metals and Nutrients 486
Metals 486
DOM, Iron, and Inorganic Phosphorus 486
DOM and Nitrogen 486
Humic Substances and Hydrophobic Contaminants 486
Concluding Remarks 487
Glossary 487
Further Reading 487
Lipids 488
Introduction 488
Essential Fatty Acids 488
Important Lipid Groups and Functions 489
Fatty Acid Transfer and Modification in the Freshwater Food Web 491
Eukaryotic Algae 491
EFA in Freshwater Fish 492
Characteristics of Food for Freshwater Fish 494
Concluding Remarks 495
Glossary 495
Further Reading 496
Relevant Websites 496
Methane 497
Introduction 497
CH4 Formation 497
Biochemical and Microbiological Aspects of Methanogenesis 497
Environmental Factors Affecting Methanogenesis 498
Spatial Distribution of Methanogenesis in Freshwater Environments 499
CH4 Oxidation 500
Aerobic Methane Oxidation 500
Environmental Factors Affecting CH4 Oxidation 500
Anaerobic CH4 Oxidation 500
Spatial Distribution of Aquatic CH4 Oxidation 500
Aquatic CH4 Dynamics 502
CH4 Concentrations in Aquatic Environments 502
Rates of CH4 Formation and Oxidation 502
CH4 and Aquatic Food Webs 506
CH4 Emissions from Inland Waters 506
Flux Pathways 506
The Contribution of Different Flux Types and their Regulation 510
CH4 and Whole-System Carbon Cycling 518
Knowledge Gaps 518
See also 518
Further Reading 519
Natural Organic Matter 520
Introduction 520
Definitions 520
Inventories and Fluxes of NOM 520
Isolation of NOM 522
Solid Phase Extractions of NOM 522
Membrane Isolation of NOM 523
Coupled Reverse Osmosis and Electrodialysis 524
Molecular Weights of NOM 524
Non-Colligative Methods 525
Colligative Methods 525
Elemental Composition of NOM 525
Redfield Biomass 526
Oxidation State of Organic Carbon 527
Unsaturation 528
Acidic Functional Groups of NOM 529
13C NMR Spectroscopy of NOM 530
Integrated Description of NOM 531
Further Reading 532
Organic Nitrogen 534
Introduction 534
Dissolved Nitrogen in Aquatic Environments 534
Definition of Nitrogen Pools 534
DON vs DIN 534
Natural DON Compounds 535
Composition and Detection 535
Specific DON Compounds 535
Dissolved Free and Combined Amino Acids 538
Amino Acids in a Stratified Lake 538
Composition of DFAA 539
Composition of DCAA 539
Nonprotein Amino Acids 540
Other DON Compounds 540
Glucosamine and Other Amino Sugars 540
Dissolved RNA and DNA 541
Urea 542
Methylamines 542
Humic Matter 542
Sources of DON 542
Phytoplankton 542
Bacteria 542
Protists, Zooplankton, and Fish 543
Input of DON from Atmosphere, Soil, and Sewage Discharge 543
Atmosphere 543
Soil 543
Sewage 544
Cycling of DON 544
Cycling of Specific DON Compounds 544
Uptake of DFAA by Bacteria 544
Uptake of DFAA by Microalgae 548
Uptake of Other Amino Compounds 548
Uptake of DCAA 549
Uptake of Dissolved DNA 550
Uptake of Urea 550
Uptake of Total DON 551
Bacterial DON Dynamics 551
Appendix: Methods for Studying Cycling of DON Compounds 551
Uptake of Single DON Compounds 551
Uptake of Polymer DON Compounds 552
Further Reading 553
Relevant Websites 553
Nutrient Stoichiometry in Aquatic Ecosystems 554
Introduction 554
Stoichiometric Homeostasis 554
Stoichiometry at the Organism Level 555
Primary Producers 555
Zooplankton 556
Other Aquatic Invertebrates 557
Bacteria and Protozoa 558
Fish 558
Food Quality 559
Nutrient Recycling 560
Community Dynamics 563
Whole-System Scale 563
Further Reading 565
Relevant Website 565
Redox Potential 566
Definitions and General Aspects 566
Measuring the Redox Potential 566
Redox Reactions 567
Redox Potential and Lakes 567
Stratified Lakes 567
Redox Potential around the Sediment-Water Interface 568
Redox Potential and Nutrient Cycling 569
Redox Potential and Lake Restoration 570
Redox Potential and Rivers 571
Redox Potential and Wetlands 571
Further Reading 573
Pollution and Remediation 574
Acidification 574
Introduction 574
Chemistry of Acidified Waters and Buffering Mechanisms 574
Carbonic Acid and Fresh Water 574
Definitions and Dimensions 574
Alkalinity and acidity 575
Buffering systems: the weak acids of carbon, aluminum, and iron 575
Pyrite weathering 577
Concentrations of dissolved substances in acid waters 577
Types and Extent of Acid Waters 577
Atmospheric Deposition and Acid Rain 577
Acid Mine Drainage (AMD) 580
Drainage from Acid Sulfate Soils 580
The case of western Finland 581
The case of Australia 581
Volcanic Waters and Crater Lakes 581
Biological Effects of Acidification 581
Success of Countermeasures and Long-Term Developments 582
Rain-Acidified Waters 582
Acid Mine Drainage and Acid Sulfate Soils 582
Lake Orta: Acidified by Industrial Waste and Remediated by Liming 583
Conclusions 583
Glossary 583
Further Reading 584
Relevant Websites 585
Aquatic Ecosystems and Human Health 586
Introduction 586
Physical Threats to Human Health in Inland Waters 586
Waterborne Disease Associated with Inland Waters 586
Sources of Pathogens and Toxins: Pollution in Inland Waters 588
Fecal Pollution 588
Animals (wildlife, farm animals, pets) 588
Animal feeding operations 588
Humans 589
Septic tank systems 589
Wastewater treatment plants 590
Combined sewer overflows (CSOs) and sanitary sewer overflows (SSOs) 590
Chemical Toxins and Fish Consumption 590
Heavy metals 590
Polychlorinated biphenyls (PCBs) 591
Dichlorodiphenyltrichloroethane (DDT) 591
Protecting Human Health 591
Water Quality Standards: Monitoring Fresh Waters 591
Water Purification and Outdoor Recreation 592
General Safety 592
Conclusion 592
Glossary 592
Further Reading 593
Relevant Websites 593
Bioassessment of Aquatic Ecosystems 594
Why Biological Assessment and What is It? 594
Choices in Approach to Bioassessment 594
History of Bioassessment 596
1900-1950 596
1950-1970 597
1970-2002 597
Types of Bioassessment Studies 598
Biota Used in Bioassessments 598
Examples of Bioassessment Programs - See above in History 599
Further Reading 600
Deforestation and Nutrient Loading to Fresh Waters 602
Introduction 602
Factors Controlling Nutrient Loading in Fresh Waters 602
Dissolved Nutrients 602
Nutrients in Particulate Form 602
Effects of Deforestation on the Factors Controlling Freshwater Nutrient Loads 608
Dissolved Nutrients 608
Effects on geological weathering 608
Effects on atmospheric precipitation/climate 608
Effects on precipitation chemistry and acidity 608
Effects on hydrology 608
Effects on temperature 609
Effects on terrestrial biological processes 609
Chemical uptake 609
Chemical transformations 609
Production of soluble chemicals 610
Effects on physical-chemical reactions in the soil 610
Effects on processes within aquatic ecosystems 610
Other factors contributing to the variable effects of deforestation on nutrient loading 611
Nutrients in Particulate Form 612
Effects on Watershed Topography, Soil Erodibility, Precipitation Characteristics, and Watershed Susceptibility to Mass Wasting 612
Effects on Stream-Channel Characteristics 613
Effects on Proximity of Vegetation to Surface Water 613
Effects on Extent of Roading 613
Conclusions 614
Knowledge Gaps 616
General Effects of Deforestation on Freshwater Nutrient Loading 616
Further Reading 617
Relevant Websites 617
Distribution and Abundance of Aquatic Plants - Human Impacts 618
Introduction 618
Eutrophication 618
Effects of Increased Nutrients on Primary Producers 618
Feedbacks between Plants and Algae and Trophic Interactions 620
Effects of Watershed and Shoreline Development on Aquatic Plant Communites 621
Increased Ultraviolet Radiation 621
Acid Rain 621
Chemical Pollutants 622
Increased Carbon Dioxide 622
Complex Interactions - Increased CO2, Acidification and Eutrophication 622
Complex Interactions - Plants, Algae, Nutrients, Carbon and Consumers 623
Invasive Species Introductions 623
Aquatic Plant Management Activities 623
Mechanical Control 624
Physical Control 624
Biological Control 624
Chemical Control 624
Conclusion 626
Further Reading 626
Effects of Climate Change on Lakes 628
Introduction 628
Physical Effects of Climate Change 628
Basin Integrity 628
Water Balance 629
Ice Cover 629
Temperature and Stratification 630
Chemical Effects of Climate Change 630
In-Lake Effects 630
Catchment Effects 631
Biological Effects of Climate Change 631
Ecosystem Integrity 631
Vertical Habitat Structure 631
Photosynthetic Communities 632
Fish Communities and Migration 632
Microbial Processes 633
Further Reading 633
Eutrophication 634
Introduction 634
Origins and Evolution of the Eutrophication Concept 634
Current Understanding and Management of Eutrophication 634
Sources of Nutrients to Inland Surface Waters 634
Nitrogen and Phosphorus are Essential Growth- Limiting Nutrients 637
Nutrient Loading Models 637
Effects of Eutrophication on Water Quality 638
Factors that Modify the Local Expression of Eutrophication 638
Effects of salinity 638
Effects of inorganic turbidity and dissolved organic color 638
Effects of hydrology 640
Effects of vascular plants (macrophyte vegetation) 640
Effects of food web structure 640
Alternative stable states 641
Correcting the problem: Eutrophication control, restoration, and management 642
Conclusions 642
Knowledge Gaps 642
Causes and Composition of Harmful Algal Blooms 642
Health Risks 644
Interactions with other Pollutants and Environmental Stressors 644
General Effects of Eutrophication 644
Glossary 645
Further Reading 645
Relevant Websites 646
Fires 647
Introduction 647
The Structure of Wildfire 647
Fire Intensity 647
Fire Severity 647
Fire Size 648
Fire Frequency 648
Wildfires as an Ecological Impact on Aquatic Systems 648
Pre-Fire Considerations 649
Watershed Slope 650
Catchment Size 650
System Morphology 650
Soil Characteristics 650
Baseline Water Chemistry 650
Weather Patterns 650
Timing 651
Fuel Load and Forest Age 651
Canopy Type 651
Post-Fire Impacts 651
Immediate Effects: 0-5 Years 651
Nutrient cycling 651
Infiltration and runoff 652
Sedimentation and erosion 653
Biota 653
Intermediate Effects: up to 10 Years 658
Nutrient cycling 658
Infiltration and runoff 658
Sedimentation 658
Biota 658
Long-Term Effects: 10{/tf= 658
Summary 659
Glossary 660
Further Reading 660
Relevant Websites 660
Floods 661
Definition of Flood 661
Causes and Effects of Floods 661
Flood Costs and Mitigation 663
Further Reading 664
Mercury Pollution in Remote Fresh Waters 665
Introduction 665
The Distribution of Mercury in Fresh.Waters 665
Lake Water and Sediments 665
Hypolimnetic Enrichment 665
Seasonality 666
Biota 667
Mass Balances for Mercury 669
Annual Budgets for Total Mercury 669
Seasonal Budgets for Methylmercury 670
Methylation Pathways 671
Hg(II) Methylation 672
MeHg Demethylation 672
The Aquatic Mercury Cycle 672
Remediation Strategies 673
Further Reading 674
Pollution of Aquatic Ecosystems I 675
Introduction 675
The Evolution of Human Societies and Water Pollution 675
Identifying Sources of Pollution 675
Point Source Pollution 676
Nonpoint Source Pollution 677
Specific Sources of Aquatic Pollution 677
Oxygen Demand in Aquatic Ecosystems 679
Chemical Oxygen Demand 680
Biological Oxygen Demand 681
Factors Affecting Oxygen Demand 681
Restoration Techniques to Avoid Low Oxygen 681
Nutrients in Aquatic Ecosystems 682
Eutrophication, Supply Ratios, and Species Composition 682
Other Consequences of Eutrophication 683
Reducing Nutrients in Aquatic Ecosystems 683
Restoring Aquatic Ecosystems 683
Conclusions 683
Glossary 684
Further Reading 684
Relevant Websites 684
Pollution of Aquatic Ecosystems II: Hydrocarbons, Synthetic Organics, Radionuclides, Heavy Metals, Acids, and Thermal Pollution 685
Introduction 685
Hydrocarbons 685
Organic Solvents 685
Petroleum Hydrocarbon Oils 685
Polycyclic Aromatic Hydrocarbons 686
Synthetic Organic Chemicals 687
Polychlorinated Biphenyls 687
Polybrominated Diphenyl Ethers 688
Pesticides 688
Unwanted Waste Byproducts 689
Chemicals of Emerging Concern 689
Heavy Metals 691
Mercury 691
Other Toxic Elements 692
Radionuclides 692
Thermal Pollution 693
Further Reading 693
Relevant Websites 693
Vector-Borne Diseases of Freshwater Habitats 694
Introduction 694
Human Diseases and Freshwater Vectors 694
Insect Vectors of Human Disease 695
Snails and Crustacenas as Intermediate Hosts of Human Disease 696
Habitats of Human-Disease Vectors 697
Vector Control Strategies 698
Human Culture, Freshwater Vectors and Disease 700
Glossary 701
Further Reading 702
Subject Index 704