A survey of the Ohio, Missouri and Upper Mississippi Rivers revealed large (five-fold) differences in river-wide average chlorophyll a (CHLa).  Inter-annual variation was low suggesting that basin- specific factors exert greater control over river-wide CHLa than regional-scale processes influencing inter-annual climatic variability and discharge.  Inter-river differences in average CHLa followed differences in nutrient concentrations.  Highest average concentrations of CHLa and nutrients were observed in the Mississippi with lowest values measured in the Ohio.  In the Missouri River, CHLa and nutrient concentrations were low in the upper, inter-reservoir zone and higher in the lower, channelized zone.  Despite these trends, regression models based on nutrients alone accounted for only a small proportion of inter- and intra- river variation in CHLa.  Models that incorporated both light and nutrient effects had greater predictive power accounting for ca. 60% of the variation in CHLa.  Inferred estimates of filtration rates by benthic and pelagic consumers suggest that microzooplankton (principally rotifers) were the dominant grazers.  Macrozooplankton and Dreissenid mussels were common in two of the three rivers (Ohio and Upper Mississippi) but their inferred filtration rates were small (<5% d^-1) compared to the microzooplankton (16-45% d^-1).  CHLa and POC were positively correlated in all three rivers suggesting that phytoplankton were important contributors to particulate organic matter.  Tributaries and floodplain habitats were found to be minor sources of CHLa but may be important in providing inocula of phytoplankton to the mainstem.