The Hudson River Estuary, first published in 2006, is a scientific biography with relevance to similar natural systems.

1. The Hudson River Estuary: executive summary; Part I. Geological, Physical and Chemical Setting of the Hudson: 2. The Hudson River Valley: geological history, landforms and resources; 3. The Physical oceanography processes of the Hudson River; 4. Sedimentary processes in the Hudson River Estuary; 5. Benthic habitat mapping in the Hudson River Estuary; 6. Reconstructing sediment chronologies in the Hudson River Estuary; 7. Major ion geochemistry and drinking water supply issues in the Hudson River Basin; Part II. Primary Production, Microbial Dynamics and Nutrient Dynamics of the Hudson: 8. Bacterial abundance, growth and metabolism in the tidal freshwater Hudson River; 9. Primary production and its regulation in the tidal-freshwater Hudson River; 10. Wastewater and watershed influences on primary productivity and oxygen dynamics in the lower Hudson River Estuary; 11. Modeling primary production in the lower Hudson River Estuary; Part III. Hudson River Communities, Food Webs and Fisheries: 12. Larval migrations between the Hudson River Estuary and New York Bight; 13. The diadromous fish fauna of the Hudson River: life histories, conservation concerns, and research avenues; 14. Fisheries of the Hudson River Estuary; 15. The role of tributaries in the biology of Hudson River fishes; 16. Ecology of the Hudson River zooplankton community; 17. Submerged macrophyte distribution and function in the tidal freshwater Hudson River; 18. Long-term and large-scale patterns in the benthic communities of New York Harbor; 19. The benthic animal communities of the tidal-freshwater Hudson River Estuary; 20. Tidal wetlands of the Hudson River 21. Alien species in the Hudson River; Part IV. Contaminants and Management Issues of the Hudson River Estuary: 22. The history and science of managing the Hudson River; 23. Hudson River sewage inputs and impacts: past and present; 24. PCBs in the upper and tidal-freshwater Hudson River Estuary: The science behind the dredging controversy; 25. Transport, fate and bioaccumulation of PCBs in the lower Hudson River; 26. Contaminant chronologies from Hudson River sedimentary records; 27. Atmospheric deposition of PCBs and PAHs to the New York Harbor Estuary; 28. Toxic substances and their impacts on human health in the Hudson River watershed; 29. Impacts of piers on juvenile fishes in the lower Hudson River; 30. Toxic responses of Hudson River populations to chemical contaminants.