Increased frequency of heavy rainfall caused by climate change may affect nutrient transport from forests and agricultural lands into downstream rivers. However, little information is available on how the effects of land cover on nutrient concentrations in the downstream rivers change depending on hydrological conditions. To elucidate this, we investigated the effects of changes in precipitation and river discharge on the relationship between river nutrient concentrations (total nitrogen, total phosphorus, nitrate, and phosphate) and land cover in eight subbasins of the Hii River basin, western Japan. We hypothesized that coniferous forests and agricultural lands including poorly managed ones, which require thinning and fertilizer management, respectively, contribute to increases in nutrient concentrations in downstream rivers during storms. Linear mixed‐effects model analyses based on 18‐year observation data were used for testing the hypothesis. Results revealed that the slopes of the multiple regression analysis between nutrient concentrations and coniferous and broad‐leaved forest area ratios were negative and decreased with increasing daily precipitation. This suggests that forests contributed to the dilution of river nutrient concentrations during storms regardless of whether they were coniferous or broad leaved. In contrast, the slope of regression between nutrient concentrations and agricultural area ratio revealed the opposite trend, indicating that even a small percentage of agricultural area makes a large contribution to increases in nutrient concentrations as precipitation increases. Our results imply that storm runoff in response to rainfall results in an elevated supply of nitrogen and phosphorus attached to arable soils to the river.