Nitrogen and phosphorus budgeting is considered to be a useful tool for policy makers and stakeholders when dealing with nutrient contamination issues. Although a variety of budgeting approaches have been employed in countries affected by this problem, the direct comparison of possible options for the same area is quite limited. The current study offers a detailed insight into the estimations of nutrient loads and their distribution between different sources for a middle-sized agricultural catchment, with the use of two approaches: mass balance method and SWAT modelling. As a result of their comparison, both methods revealed similar contributions of analysed nutrient sources, although the absolute loads were heterogeneous, which stems from drawbacks related to the quality of the monitoring data, the performance of the model and omission of some catchment processes. However, in light of the performed comparison, we suggest a hybrid solution, combining the best features of both approaches.