Nutrient retention in lakes and rivers is an essential regulating ecosystem service that protects downstream water bodies from nutrient excess, reducing anthropic impacts on aquatic habitats. Quantifying nutrient retention in freshwaters is important for basin management, but difficult as retention depends, among other things, on the spatial and temporal scales of interest. This study aimed at assessing freshwater nutrient retention in contemporary Europe at continental scale with an ensemble modeling exercise. We used the conceptual model GREEN, changing lake retention according to alternative formulations, generating six model versions for total nitrogen (TN), and seven for total phosphorus (TP). All versions were calibrated independently in six European regions, defined by the sea to which land drained to. Parameter sets that performed well in overall calibration and at stations downstream lakes formed the ensembles that were used to quantify freshwater retention over a decade (2012–2021). Ensemble median river retention was about 10% of incoming TN load and 6% TP load. Median lake retention was about 4% for TN and 6.5% for TP. Median freshwater retention amounted to 170 kg N yr−1 and 7.2 kg P yr−1 per km2 of drainage area. European freshwaters retained about 16% of incoming nitrogen and 13% of incoming phosphorus loads, preventing about 1066 kt N yr−1 and 49 kt P yr−1 to reaching the coastline. Nitrogen retention mostly occurred in rivers, whereas phosphorus retention occurred predominantly in lakes, however important regional differences were noted. The assessment likely underestimates the overall role of freshwater nutrient retention, as secondary streams, wetlands, and ponds were not considered explicitly. Nevertheless, it provides quantitative references for accounting of freshwaters ecosystem services at continental scale.