In this study, we investigated the relationships between stream water chemistry and watershed characteristics (topography--mean altitude and slope; climate--mean annual temperature and precipitation; geology--geochemical reactivity; land cover; inhabitation--population density, road density and number of municipalities). We analyzed the concentrations of the major anions (Cl, F, NO3, SO4, SiO2), cations (Ca, Mg, Na, K, Mn, Fe, Al), trace elements (Li, Sr, Cu), ABS245, TDP (total dissolved phosphorus), pH, and conductivity at 3,220 diverse watersheds covering a wide variety of watershed characteristics in the Czech Republic. We used marginal and partial multivariate analyses to reveal the most important variables. The partial analysis showed that only 14% of the variance could be assigned to a specific factor and that 41% of the variance is shared among the factors, which indicated complex interactions between the watershed characteristics.