Across the distances spanned by large rivers, there are important differences in catchment characteristics, tributary inputs, and river morphology that may cause longitudinal changes in nutrient, chlorophyll, and suspended solids concentrations. We investigated longitudinal and seasonal patterns in the Upper Mississippi River (UMR) using long-term data (1994-2005) from five study reaches that spanned 1300 km of the UMR. Lake Pepin, a natural lake in the most upstream study reach, had a clear effect on suspended material in the river. Suspended solids and total phosphorus (TP) concentrations were substantially lower downstream of the lake and percent organic material (OM%) in suspension was higher. Below L. Pepin, mean total and organic suspended solids (TSS, OSS) and TP increased downriver and exhibited approximately log-linear relationships with catchment area, whereas OM% declined substantially downriver. Despite the downriver increase in TSS and OSS, concentrations similar to those above L. Pepin do not occur until ~370 km downriver indicating the extent of the influence of L. Pepin on the UMR. Chlorophyll concentrations were lower in the most downstream study reach, likely reflecting the shorter residence time and poor light climate, but there was not a consistent longitudinal decline in chlorophyll across the study reaches. Dissolved silica (DSi), DSi:TN, and DSi:TP declined downriver suggesting that DSi uptake and sedimentation by river phytoplankton may be reducing DSi transport in the river, and indicating that the eutrophication of the river may contribute to a reduction of DSi export to the Gulf of Mexico. ?? 2010 US Government: USGS.