Tropical coastal ecosystems are declining globally due to human activities, primarily poor water quality from land-based sources. This review highlights the impact of sediments, nutrients, chemicals, and pathogens on coastal ecosystems, especially coral reefs, and on human health through disease transmission, reduced food availability, and food poisoning. Integrated watershed management (IWM) is proposed as a solution, requiring a multi-sector, systems approach that includes environmental, agricultural, public health, and water sectors. Key IWM actions can support sustainable development goals for both coastal ecosystems and human populations.