Global climate and environmental change affect the biogeochemistry and ecology of aquatic systems mostly due to a combination of natural and anthropogenic factors. The latter became more and more important during the past few thousand years and particularly during the ‘Anthropocene’. However, although they are considered important in this respect as yet much less is known from tropical than from high latitude coasts. Tropical coasts receive the majority of river inputs into the ocean, they harbor a variety of diverse ecosystems and a majority of the population lives there and economically depends on their natural resources. This review delineates the biogeochemical response of coastal systems to environmental change and the interplay of natural and anthropogenic control factors nowadays and in the recent geological past with an emphasis on tropical regions. Weathering rates are higher in low than in high latitude regions with a maximum in the SE Asia/Western Pacific region. On a global scale the net effect of increasing erosion due to deforestation and sediment retention behind dams is a reduced sediment input into the oceans during the Anthropocene. However, an increase was observed in the SE Asia/Western Pacific region. Nitrogen and phosphorus inputs into the ocean have trebled between the 1970s and 1990s due to human activities. As a consequence of increased nutrient inputs and a change in the nutrient mix excessive algal blooms and changes in the phytoplankton community composition towards non-biomineralizing species have been observed in many regions. This has implications for foodwebs and biogeochemical cycles of coastal seas including the release of greenhouse gases. Examples from tropical coasts with high population density and extensive agriculture, however, display deviations from temperate and subtropical regions in this respect. According to instrumental records and observations the present-day biogeochemical and ecological response to environmental change appears to be on the order of decades. A sediment record from the Brazilian continental margin spanning the past 85,000years, however, depicts that the ecosystem response to changes in climate and hydrology can be on the order of 1000–2000years. The coastal ocean carbon cycle is very sensitive to Anthropocene changes in land-derived carbon and nutrient fluxes and increasing atmospheric carbon dioxide. As opposing trends in high latitude regions tropical coastal seas display increasing organic matter inputs and reduced calcification rates which have important implications for calcifying organisms and the carbon source or sink function of the coastal ocean. Particularly coral reefs which are thriving in warm tropical waters are suffering from ocean acidification. Nevertheless, they are not affected uniformly and the sensitivity to ocean acidification may vary largely among coral reefs. Therefore, the prediction of future scenarios requires an improved understanding of present and past responses to environmental change with particular emphasis put on tropical regions.