Karst watersheds are a major source of drinking water in the European Alps. These watersheds exhibit quick response times and low residence times, which might make karst aquifers more vulnerable to elevated nitrogen (N) deposition than nonkarst watersheds. We summarize 13 years of monitoring NO 3 − , NH 4 + , and total N in two forest ecosystems, a Norway spruce (Picea abies (L.) Karst.) forest on Cambisols/Stagnosols (IP I) and a mixed beech (Fagus sylvatica L.) spruce forest on Leptosols (IP II). N fluxes are calculated by multiplying concentrations, measured in biweekly intervals, with hydrological fluxes predicted from a hydrological model. The total N deposition in the throughfall amounts to 26.8 and 21.1 kg/ha/year in IP I and IP II, respectively, which is high compared to depositions found in other European forest ecosystems. While the shallow Leptosols at IP II accumulated on average 9.2 kg/ha/year of N between 1999 and 2006, the N budgets of the Cambisols/Stagnosols at IP I were equaled over the study period but show high inter-annual variation. Between 1999 and 2006, on average, 9 kg/ha/year of DON and 20 kg/ha/year of DIN were output with seepage water of IP I but only 4.5 kg/ha/year of DON and 7.7 kg/ha/year of DIN at IP II. Despite high DIN leaching, neither IP I nor IP II showed further signs of N saturation in their organic layer C/N ratios, N mineralization, or leaf N content. The N budget over all years was dominated by a few extreme output events. Nitrate leaching rates at both forest ecosystems correlated the most with years of above average snow accumulation (but only for IP I this correlation is statistically significant). Both snow melt and total annual precipitation were most important drivers of DON leaching. IP I and IP II showed comparable temporal patterns of both concentrations and flux rates but exhibited differences in magnitudes: DON, NO 3 − , and NH 4 + inputs peak in spring, NH 4 + showed an additional peak in autumn; the bulk of the annual NO 3 − and DON output occurred in spring; DON, NO 3 − , and NH 4 + output rates during winter months were low. The high DIN leaching at IP I was related to snow cover effects on N mineralization and soil hydrology. From the year 2004 onwards, disproportional NO 3 − leaching occurred at both plots. This was possibly caused by the exceptionally dry year 2003 and a small-scale bark beetle infestation (at IP I), in addition to snow cover effects. This study shows that both forest ecosystems Water Air Soil Pollut (2011) 218:633-649