The aim of the study was to determine the relationship between changes in the load of nitrogen and phosphorus of agricultural origin in the catchment area and other structural and functional parameters, including mainly agricultural production factors and the overall land use structure. The study area comprises two catchment areas located in the southern part of the Małopolska Province: the upper Dunajec catchment area and the upper Raba catchment area. The study analysed agricultural parameters and land use structure, and performed a multiple analysis of the parameters studied. Structural changes in the upper Dunajec and Raba river catchments in recent years have affected many areas of social and economic life. Among other things, the size and nature of agricultural production have changed dynamically, resulting in long-term changes in land use and spatial distribution. Based on Spearman's rank analysis, it was found that among the relationships between the studied factors, the least significant were the relationships between the N and P balance and the area of pastures, and, to some extent, the utilisation index W. However, a close collinear relationship was noted between the reduction in the N and P balance and a reduction in livestock numbers, as well as a significant reduction in both mineral and natural fertilisation. The dominant importance of these factors in shaping N and P balances also resulted from the regression relationships determined.