Abstract. Intensive farming has severe impacts on the chemical status of groundwater and streams and consequently on the ecological status of dependent ecosystems. Eutrophication is a widespread problem in lakes and marine waters. Common problems are hypoxia, algal blooms, fish kills, and loss of water clarity, underwater vegetation, biodiversity and recreational value. In this paper we evaluate the nitrogen (N) and phosphorus (P) concentrations of groundwater and surface water in a coastal catchment, the loadings and sources of N and P, and their effect on the ecological status of an estuary. We calculate the necessary reductions in N and P loadings to the estuary for obtaining a good ecological status, which we define based on the number of days with N and P limitation, and the corresponding stream and groundwater threshold values assuming two different management options. The calculations are performed by the combined use of empirical models and a physically based 3-D integrated hydrological model of the whole catchment. The assessment of the ecological status indicates that the N and P loads to the investigated estuary should be reduced to levels corresponding to 52 and 56% of the current loads, respectively, to restore good ecological status. Model estimates show that threshold total N (TN) concentrations should be in the range of 2.9 to 3.1 mg l⁻¹ in inlet freshwater (streams) to Horsens estuary and 6.0 to 9.3 mg l⁻¹ in shallow aerobic groundwater (∼ 27–41 mg l⁻¹ of nitrate), depending on the management measures implemented in the catchment. The situation for total P (TP) is more complex, but data indicate that groundwater threshold values are not needed. The stream threshold value for TP to Horsens estuary for the selected management options is 0.084 mg l⁻¹. Regional climate models project increasing winter precipitation and runoff in the investigated region resulting in increasing runoff and nutrient loads to the Horsens estuary and many other coastal waters if present land use and farming practices continue. Hence, lower threshold values are required in many coastal catchments in the future to ensure good status of water bodies and ecosystems.