Agricultural and rural land management practices can have a significant impact on the health of river ecosystems. In this study, our goal was to quantify the extent of land use influence on river water quality at two catchments in rural North Wales, Conwy and Clwyd. Stream water samples were collected bi‐weekly from five sampling sites over a three‐month period (September–November 2018) and analyzed in the laboratory to measure six water quality variables, namely, pH, electrical conductivity (EC), phosphorus, nitrate and ammonium concentrations, and bacterial coliform count. We then quantified their relationships with dominant land cover of the contributing catchments using two different land cover classification systems. Significant differences (p < 0.05) were observed across the sampling sites for pH, EC, nitrate and phosphorus concentration, and coliform count. Strong correlations were observed between pH and the proportion of Acid Grassland, and between nitrate levels and the proportion of Improved Grassland in the catchment. The presence of high‐quality agricultural land correlated positively with nitrate and phosphorus concentrations and bacterial coliform count. Conversely, dominance of poor quality agricultural land correlated with lower levels of all the measured water quality indicators. Our results suggest that the proportion of high‐quality agricultural land is a reliable indicator of stream water quality in rural catchments, most likely linked to intensive farming practices.