Losses of phosphorus (P) and nitrogen (N) have important influences on in-lake concentrations and nutrient loading to downstream ecosystems. We performed a series of mesocosm experiments along a latitudinal gradient from Sweden to Greece to investigate the factors influencing N and P loss under different climatic conditions. In six countries, a standardised mesocosm experiment with two water depths and two nutrient levels was conducted concurrently between May and November 2011. Our results showed external nutrient loading to be of key importance for N and P loss in all countries. Almost all dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (SRP) were lost or taken up in biomass in all mesocosms. We found no consistent effect of temperature on DIN and SRP loss but a significant, though weak, negative effect of temperature on total nitrogen (TN) and total phosphorus (TP) loss in the deeper mesocosms, probably related to higher organic N and P accumulation in the water in the warmer countries. In shallow mesocosms, a positive trend in TN and TP loss with increasing temperature was observed, most likely related to macrophyte growth.