The relationship between land use and stream chemistry is often explored through synoptic sampling of rivers at baseflow conditions. However, baseflow chemistry is likely to vary temporally and spatially with land use. The purpose of our study is to examine the usefulness of the synoptic sampling approach for identifying the relationship between complex land use configurations and stream water quality. This study compares biogeochemical data from three synoptic sampling events representing the temporal variability of baseflow chemistry and land use using R-mode factor analysis. Separate R-mode factor analyses of the data from individual sampling events yielded only two consistent factors. Agricultural activity was associated with elevated levels of Ca2+, Mg2+, alkalinity, and frequently K+, SO4(2-), and NO3-. Urban areas were associated with higher concentrations of Na+, K+, and Cl-. Other retained factors were not consistent among sampling events, and some factors were difficult to interpret in the context of biogeochemical sources and processes. When all data were combined, further associations were revealed such as an inverse relationship between the proportion of wetlands and stream nitrate concentrations. We also found that barren lands were associated with elevated sulfate levels. This research suggests that an individual sampling event is unlikely to characterize adequately the complex processes controlling interactions between land use and stream chemistry. Combining data collected over two years during three synoptic sampling events appears to enhance our ability to understand processes linking stream chemistry and land use.