In aquatic ecosystems, nitrogen (N) loading is mitigated in redox transition zones principally through the processes of denitrification and anaerobic oxidation of ammonium (anammox). Here, we investigate the N cycling processes in the water column of a seasonal stratified lake influenced by benthic processes in Southern Germany (Fohnsee) during the development of the vertical redox stratification between April and September. Concentration profiles and stable isotope compositions of NO₃⁻ and NH₄⁺ together with numerical modeling and quantification of the hydrazine synthase gene (hzsB) and nitrite reductase (nirK and nirS) genes were used to identify the predominant nitrogen-transformation processes at lake Fohnsee throughout the spring and summer periods. Water chemistry data, quantitative polymerase chain reaction analysis and increases of δ¹⁵N and δ¹⁸O values of nitrate from 7.0‰ to 41.0‰ and 2.0‰ to 28.0‰, respectively, showed that nitrate reduction to nitrite and NO occurs in an upward moving zone of the water column from June to September following the displacement of the oxycline caused by thermal stratification. We also observed an increase in δ¹⁵N of ammonium from 15‰ to 28‰ in the anoxic water column. Modeling results suggest that this shift in δ¹⁵N-NH₄⁺ is predominantly controlled by mixing between ammonium stemming from the oxic water column with δ¹⁵N values of 25‰ and ammonium that is likely formed in the lake sediments by oxidation of organic matter with δ¹⁵N values of 11‰. Observed gene abundances (hzsB, nirK, and nirS) in lake water samples collected in June and July indicated the co-occurrence of nitrate reduction and low rates of anammox, while the presence of sulfide in August and September may have inhibited the activity of anammox bacteria near the sulfate-reduction zone at the lake bottom. This study revealed temporal and spatial (e.g., depth dependent) variations in the dominant N-transformation processes in the investigated lake.