This article presents a scientific overview of the processes and the impact of environmental degradation of coastal waters due to human activities on the adjoining land. The direct effects range from eutrophication, harmful algae blooms, to hypoxia and anoxia. The indirect effects are more subtle and can also lead to the collapse of the ecosystem; such is the case of coral reefs. Engineering solutions alone are not available to prevent this degradation that can only be reversed, or prevented, using a basin-wide ecohydrology approach. Keywords: Anoxia, Coral reef, Ecosystem manipulation, Ecosystem model, Eutrophication, Fisheries, Food web, Harmful algae blooms, Hypoxia, Physics-biology links.