On a global scale tropical SE Asia is critical in terms of fluvial nutrient and sediment input into the ocean as well as in terms of human modifications of the coastal zone altering these inputs. In order to obtain information on the biogeochemistry of the Brantas River estuary and adjacent coastal waters of the Madura Strait in eastern Java, Indonesia, a densely-populated area which is strongly affected by human activities in the river catchment, we investigated water, suspended matter and sediments from estuarine and coastal waters and plants and soils from the catchment collected during the dry season. Water samples were analyzed for dissolved nutrients and phytoplankton abundance and composition. Suspended matter, sediment, plant and soil samples were analyzed for carbon, nitrogen, amino acids and stable carbon and nitrogen isotopes. Nutrient concentrations were high in the river and then decreased rapidly seaward. Runoff from agricultural soils may be a major nutrient source. Phytoplankton was dominated by diatoms and most abundant in the estuarine mixing zone. A fairly high phytoplankton abundance despite nitrate-depletion and an N/P ratio <4 in coastal waters indicates additional nitrogen sources. Biogeochemical characteristics and stable isotopes indicate the autochthonous origin of suspended organic matter (OM) during the dry season. Major part of the fluvial input appears to be trapped in the inner estuary. Similar information obtained from the analysis of sediments suggests seasonal differences in the quantity and origin of suspended sediments and OM transported by the river with high inputs into coastal waters during the rainy season, the period of peak river discharge. The amino acid composition in combination with stable isotopes indicates agricultural soils to be a major OM source during that time. A high proportion of amino acid-bound nitrogen in suspended matter and sediments and the presumed sources of dissolved nitrogen other than nitrate to sustain primary productivity in the coastal zone suggest that organic nitrogen may play a more important role for coastal food webs and the nitrogen cycle in tropical regions than previously thought.