In view of the increasing problems of waste disposal in the Netherlands, plans were made to pipeline the waste to the Ems-Dollard estuary. To evaluate the practicability a project was started with the aim to implement a simulation model of an estuary ecosystem. This model was based on the knowledge of the hydrology, geochemistry and biology of the Ems estuary. For this approach data of the abiotic and biotic environment were collected in studies of the Ems estuary and are presented in this report. With its comprehensive information of biological processes as food webs, biomass production and nutrient supply, as well as of sedimentological and flux parameters, this book can be considered as a general model of an estuary ecosystem.

I: Description of the Ecosystem.- 1 Modelling the Ecosystem of the Ems Estuary.- 1.1 Introduction.- 1.2 Earlier Investigations of the Ems Estuary.- 1.3 Other Models of the Ems Estuary.- 1.4 Structure of the Ecosystem Model.- 1.5 A Glimpse of the Modelling Practice.- 1.6 Simulation Hard-and Software.- 2 The Abiotic Environment.- 2.1 History.- 2.2 Topography and Morphology.- 2.3 Sediment Composition.- 2.4 Climate.- 2.5 Fresh Water Supply.- 2.6 Tide.- 2.7 Water Movement and Mixing.- 2.8 Sediment Transport and Accumulation.- 2.9 Nutrients.- 3 Biology.- 3.1 General Description of the Estuary.- 3.2 The Pelagic System.- 3.3 The Benthic System.- 3.4 The Epibenthic System.- 4 General Features in the Model.- 4.1 Universal Biological Processes.- 4.1.1 Maintenance Processes.- 4.1.2 Activity-Dependent Processes.- 4.1.3 Bookkeeping Calculations.- 4.1.4 Modelling Food Uptake.- 4.1.5 Food Selection.- 4.1.6 Food Levels.- 4.2 Compartments and Boundary Conditions.- 4.2.1 Boundaries.- 4.2.2 The Dimensions of the Compartments.- 4.2.3 Boundary Conditions.- 4.3 Forcing Functions.- 4.3.1 Temperature.- 4.3.2 Irradiance.- 4.4 The Nature and Flux of Organic Matter.- 4.4.1 Partition of Organic Matter.- 4.4.2 Transport of Organic Matter.- 4.4.3 The Nutritional Value of Detrital Organic Matter (Detritus).- II: The Blueprint of the Model.- 5 The Construction of the Transport Submodel.- 5.1 Introduction.- 5.2 Diffusive Transport.- 5.2.1 Determination of the Constants.- 5.3 Transport of Particulate Material.- 5.3.1 Description.- 5.3.2 Vertical Transport Processes: Sedimentation and Resuspension.- 5.3.3 Horizontal Transport Processes.- 5.3.4 Boundary Conditions.- 5.3.5 Calibration of the Model.- 5.3.6 Detrital Carbon in the Mud.- 6 The Construction of the Pelagic Submodel.- 6.1 Introduction.- 6.2 Phytoplankton and Nutrients.- 6.2.1 State Variables.- 6.2.2 Irradiance and Photosynthesis.- 6.2.3 Nutrients.- 6.2.4 Assimilation.- 6.2.5 Loss Terms.- 6.3 Zooplankton.- 6.3.1 Microzooplankton.- 6.3.2 Mesozooplankton.- 6.3.3 Carnivorous Zooplankton.- 6.4 Pelagic Bacteria.- 6.4.1 Biomass.- 6.4.2 Uptake.- 6.4.3 Loss Terms.- 6.5 Oxygen in the Water.- 6.5.1 Physical and Chemical Aspects.- 6.5.2 Sources and Sinks of Oxygen.- 7 The Construction of the Benthic Submodel.- 7.1 Introduction.- 7.2 Benthic Primary Producers.- 7.2.1 Vertical Distribution of Biomass.- 7.2.2 Effects of Light.- 7.2.3 Specific Growth Rate and Primary Production.- 7.2.4 Excretion and Respiration.- 7.2.5 Suspension.- 7.3 Meiofauna.- 7.3.1 Food Uptake.- 7.3.2 Loss Factors.- 7.4 Macrobenthos.- 7.4.1 Biology.- 7.4.2 Model Description: Deposit Feeders.- 7.4.3 Model Description: Suspension Feeders.- 7.5 The Spatial Structure of the Sediment and Vertical Transport.- 7.5.1 Oxygen Demand and Sulphide Production.- 7.5.2 Nondiffusive Transport Processes.- 7.5.3 Diffusive Transport Processes.- 7.5.4 The Transition of Organic Matter Between the Benthic Layers.- 7.6 Benthic Bacteria.- 7.6.1 Distribution of Biomass.- 7.6.2 Uptake of Labile Organic Carbon.- 7.6.3 Detritus and Refractive Organic Matter.- 7.6.4 Mortality and Excretion.- 7.6.5 Respiration and Temperature Correction.- 7.6.6 Conclusion.- 8 The Construction of the Epibenthic Submodel.- 8.1 The State Variables.- 8.2 The Faunal Components of the Epibenthos.- 8.3 Migration.- 8.3.1 Redistribution.- 8.3.2 Comfort Functions.- 8.3.3 Immigration.- 8.3.4 Emigration.- 8.4 Uptake of Food.- 8.4.1 Calculation of Available Food.- 8.4.2 Uptake.- 8.5 Loss Factors.- 8.5.1 Respiration and Excretion.- 8.5.2 Mortality.- 8.6 Correction for Temperature.- 8.7 The Role of Foraging Birds.- 8.7.1 Estimation of the Number of Birds in the Ems Estuary.- 8.7.2 Calculation of Available Food for Birds.- 8.7.3 Uptake by Birds.- III: Results and Analysis.- 9 Running the Model.- 9.1 The Standard Run.- 9.2 The Initial Values of the State Variables.- 9.3 Validation of the Model.- 9.3.1 The Validation Sets.- 10 Results and Analysis of the Pelagic Submodel.- 10.1 Model Results and Validation of the Standing Stocks.- 10.1.1 Primary Producers.- 10.1.2 Microzooplankton.- 10.1.3 Mesozooplankton.- 10.1.4 Carnivorous Zooplankton.- 10.1.5 Pelagic Bacteria.- 10.1.6 Oxygen.- 10.1.7 Nutrients.- 10.1.8 The Detrital State Variables (PLOC, PDET, PROC, PDROC).- 10.2 Fluxes.- 10.2.1 Validated Fluxes.- 10.2.2 Nonvalidated Fluxes.- 10.3 Sensitivity Analysis.- 10.3.1 Degradation of Algal Production by Bacteria.- 10.3.2 Growth Efficiency of Bacteria.- 10.3.3 Suspended Phytobenthos as a Food Source for Zooplankton.- 10.3.4 The Role of Microzooplankton in the Model.- 10.3.5 Regulation of the Phytoplankton Succession.- 10.4 Conclusions.- 11 Results and Analysis of the Benthic Submodel.- 11.1 The Seasonal Cycle of the State Variables.- 11.1.1 Total and Anaerobic Bacterial Biomass.- 11.1.2 Phytobenthos.- 11.1.3 Meiobenthos.- 11.1.4 Macrobenthos.- 11.1.5 Organic Matter.- 11.1.6 Sulphide and Pyrite.- 11.1.7 The Location of the Sulphide Horizon.- 11.2 The Fluxes from and to the State Variables.- 11.2.1 Validated Fluxes.- 11.3 Unvalidated Fluxes.- 11.3.1 Diet of Meiofauna.- 11.3.2 Grazing and Predation in the Benthos.- 11.3.3 Carbon Budgets of Organisms.- 11.3.4 Net Production and Productivity.- 11.3.5 Dynamics of Refractory Organic Carbon in the Sediment.- 11.4 Sensitivity Analysis of the Benthic Subsystem.- 11.4.1 Reduced Detritus.- 11.4.2 Bacterial Excretion and Efficiency.- 11.4.3 Phytobenthos Regulation.- 11.4.4 The Role of Meiobenthos in the Benthic Community.- 11.4.5 The Activity Pattern of Macrobenthos.- 11.5 Conclusions.- 12 Results and Analysis of the Epibenthos Submodel.- 12.1 Model Results.- 12.1.1 The Standing Stocks in the Five Compartments.- 12.1.2 Internal Fluxes and Productivity.- 12.1.3 Carbon Fluxes to the Epibenthic Submodel.- 12.2 Sensitivity Analysis.- 12.2.1 Varying the Immigrating Biomass.- 12.2.2 Model Runs, Partially or Wholly Excluding Epibenthos.- 12.3 Conclusions.- 13 Results and Validation of the Transport Submodel.- 13.1 Introduction.- 13.2 Transport of Dissolved Compounds.- 13.2.1 Salinity.- 13.2.2 Dissolved Organic Carbon.- 13.3 Transport of Particulate Compounds.- 13.3.1 Suspended Sediment.- 13.3.2 Particulate Organic Carbon.- 13.3.3 Suspended Matter.- 13.4 Flows and Annual Budgets.- 13.4.1 Suspended Sediment Transport.- 13.4.2 Organic Carbon Transport.- 13.5 Sensitivity Analysis.- 13.5.1 Behaviour of Particulate Matter During Transport.- 13.5.2 The Role of Imported POC in the System.- 13.5.3 The Role of Silt in the Estuary.- 13.6 Conclusions.- 14 Model Applications and Limitations.- 14.1 Introduction.- 14.2 Limitations of the Model.- 14.2.1 Category I: "Physiological" Parameters.- 14.2.2 Category II: "Structural" Parameters.- 14.2.3 Category III: "Dimensional" Parameters.- 14.3 Applications of the Model.- 14.3.1 Case 1: Reduced Organic Loading.- 14.3.2 Case 2: Applying the Ems Model to the Severn Estuary.- 14.4 Conclusions.- 15 References.- Appendix A: Parameter Descriptions and Values.- A-1: Parameters of the Physical Submodel.- A-2: Parameters of the Pelagic Submodel.- A-3: Parameters of the Benthic Submodel.- A-4: Parameters of the Epibenthic Submodel.- Appendix B: The FORTRAN Listing of the Submodels.- B-1: Subroutine BAHBOE.- B-2: Subroutine S…