Changes in the environment, aiming at agricultural intensification, progressive urbanisation and other forms of anthropopression, may cause an increase in soil erosion and a resulting increase in the pollution inflow to surface water. At the same time, this results in increased nutrient pollution of bottom sediments. In this study, the concentrations of total nitrogen (TN), total phosphorus (TP), total organic carbon (TOC), calcium (Ca), iron (Fe) and potassium (K) were analysed using bottom sediment samples collected at 39 sites located along the entire length of the Warta River and its tributaries. Agricultural use of land adjacent to rivers was found to significantly degrade sediment quality, while anthropogenic land use (as defined by Corine Land Cover classification—CLC), unlike previous studies, reduces the pollution loads in the bottom sediments. Forest use also contributes to the reduction of the pollution load in sediments. It was found that the significance of the relationship between pollutant concentrations and land use depends on the length of the river–land interface. According to the analyses, the level of correlation between the analysed constituents depends on the use of land adjacent to rivers. The impact of agricultural land use has the strongest effect in the 1 km zone and 5 km in the case of anthropogenic land use. The results showed that the variability of total phosphorus TP concentrations is strongly correlated with the variability of iron concentrations. SPI values indicate that the risk to sediment quality is low due to TOC and Fe concentrations. In contrast, the risk of sediment pollution by TN and TP shows greater differentiation. Although the risk is negligible for 40% of the samples, at the same time, for 33% of the samples, a very high risk of pollution with both TN and TP was found.