Nitrogen and phosphorus budgeting is considered to be a key tool for policy makers and stakeholders when dealing with nutrient contamination issues, however no unified method has been employed in countries affected by this eutrophication problem. 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 (static) and modelling (dynamic). Both methods revealed similar contributions of analysed nutrient sources, although the final estimates in the chosen calculation profile were divergent due to the various reasons related to the methods’ specificity. The advantages and disadvantages of both approaches have been specified in our study, and a hybrid solution on a local and country wide scale has been proposed.