Processes involving surface water erosion are crucial to the functioning of ecological systems and river-scale management. However, these processes are not well understood at the regional and global levels, and forested agricultural catchments have undergone major degradation because soils in river valleys are continuously inundated with rainwater. Most Carpathian catchments, particularly those at lower elevations, are used for forest or agricultural purposes, which experience the leaching of inorganic nutrients and fluxes of total suspended sediments (TSS). The objective of the current study was to investigate the distribution of inorganic nutrients and TSS in waterways draining into flysch catchments by using a new SWAT+ tool. The highest concentrations of inorganic nutrients were recorded in the main watercourse and in the outflows from the catchments. Nevertheless, the same trend was not observed for the TSS concentrations. Moreover, statistically significant relationships were revealed between agricultural use and N-NO ₃ ^- ion concentrations and between permanent grasslands and P- PO ₄ ^3- anions. The SWAT+ model can be a valuable tool for studying TSS distributions and inorganic nutrient leaching.