The impact of nonpoint-source pollution on surface waters in agricultural watersheds is an emerging environmental issue. As part of the U.S. Geological Survey National Water Quality Assessment program in the Hudson River Basin, Canajoharie Creek was monitored for seasonal and spatial patterns of nutrient chemistry from March 1993 to January 1996. Nitrate and silica concentrations in Canajoharie Creek suggest that seasonal and spatial variations of these nutrients are dominated by biological processes, particularly uptake by phytoplankton. Observed concentration patterns were more typical of those observed in much larger, low-gradient streams. The median nitrate and silica concentrations in Canajoharie Creek were significantly lower from April through November than during winter. Concentrations of both constituents declined downstream from the headwaters during base-flow conditions in June 1995. Groundwater and surface water chemistry data support biological causes for downstream decreases in silica. The strong correlation between nitrate and silica in samples collected along the mainstem suggests that most of the nitrate decrease is due to uptake by diatoms. Downstream patterns of chlorophyll-a in phytoplankton strongly suggest the conversion of in-stream nutrients to algal biomass. Data collected from Canajoharie Creek outlet during the northeast drought of 1995 indicate that silica concentrations in May had possibly declined to a level that adversely affected the diatom community. This decline in the diatom population and subsequent resurgence is inferred from a sharp rise in silica concentrations between May and July and a reversal of this trend from mid-July through October without associated changes in hydrology.