1. Introduction Part I: Physical Environment 2. Physical Parameters and Energy State 3. Substrate - Controlling the Benthic Component 4. Water Composition - Management of Salinity, Hardness, and Evaporation 5. The Input of Solar Energy - Lighting and New Possibilities 6. The Input of Organic Energy - Particulates and Feeding Part II: Biochemical Environment 7. Metabolism - Respiration, Photosynthesis, and Biological Loading 8. Organisms and Gas Exchange - Oxygen, Carbon Dioxide, pH, and Alkalinity 9. Primary Nutrients - Nitrogen, Phosphorus, and Silica 10. Biomineralization and Calcification - A Key to Biosphere and Ecosystem Function 11. Control of the Biochemical Environment - 3D Potential for Algal Turf Scrubbing Part III: Biological Structure 12. Community Structure - Biodiversity in Model Ecosystems 13. Thermogeography - The Distribution of Organisms Along Coasts 14. Trophic Structure - Ecosystems and Dynamics of Food Chains 15. Primary Producers - Bottom-Growing Plants 16. Herbivores 17. Carnivores 18. Plankton and Planktivores 19. Detritus and Detritivores 20. Symbionts and Other Feeders Part IV: Ecological Systems in Microcosms, Mesocosms, and Aquaria 21. Models of Coral Reef Ecosystems 22. Subarctic/Boreal Microcosm - Applications of New Research 23. Estuaries - Ecosystem Modelling and Restoration 24. Freshwater Ecosystem Models 25. Research Systems in Microcosms Part V: The Environment and Ecological Engineering 26. Organisms and Natural Products 27. Large Scale Water Quality Management with Solar Energy Capture Part VI: Synthesis 28. Microcosms, Mesocosms, and Macrocosms - Building and Restoring Ecosystems and the Biosphere