A geochemical analysis of the Raritan estuary during high and low river flow is presented. Several statistical and graphical approaches, in addition to a hydrodynamic model of the Raritan estuary, are used to demonstrate the effects of lateral inputs on trace-element distribution in a complicated fluvial-marine system. Results from factor and cluster analysis show that nutrient-salinity distributions on both sampling dates are controlled primarily by freshwater-saltwater mixing. Industrial and municipal waste sources within the estuary are important in controlling dissolved organic carbon (at low flow) and dissolved and bottom sediment trace metals. Biological and physico-chemical reactions have a significant, but secondary effect on nutrient and trace-metal distributions with salinity. Apparent flux calculations and property-property plots show that for dissolved phosphate, nitrate and inorganic carbon, the Raritan estuary can be divided into two mixing zones, with the Raritan River controlling nutrient concentrations in the lower-salinity stretches and the South River controlling their distributions at intermediate and higher salinities. High enrichment factors of most metals in estuary bottom sediment reveal that this is an important and semi-permanent sink for trace metals in the Raritan system. Previous work on suspended sediment in the estuary and river substantiates that this load is also an important sink for trace metals; however, many of these metals are in leachable modes which are more susceptible to release and incorporation into the food chain. ?? 1990.