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Nitrogen and phosphorous loading drives eutrophication of aquatic systems. Lakes and reservoirs are often effective N and P sinks, but the variability of their biogeochemical dynamics is still poorly documented, particularly in tropical systems. To contribute to the extending of information on tropical reservoirs and to increase the insight on the factors affecting N and P cycling in aquatic ecosystems, we here report on a long-term N and P mass balance (2003–2018) in Valle de Bravo, Mexico, which showed that this tropical eutrophic reservoir lake acts as a net sink of N (−41.7 g N m−2 y−1) and P (−2.7 g P m−2 y−1), mainly occurring through net sedimentation, equivalent to 181% and 68% of their respective loading (23.0 g N m−2 y−1 and 4.2 g P m−2 y−1). The N mass balance also showed that the Valle de Bravo reservoir has a high net N atmospheric influx (31.6 g N m−2 y−1), which was 1.3 times the external load and likely dominated by N2 fixation. P flux was driven mainly by external load, while in the case of N, net fixation also contributed. During a period of high water level fluctuations, the net N atmospheric flux decreased by 50% compared to high level years. Our results outlining water regulation can be used as a useful management tool of water bodies, by decreasing anoxic conditions and net atmospheric fluxes, either through decreasing nitrogen fixation and/or promoting denitrification and other microbial processes that alleviate the N load. These findings also sustain the usefulness of long-term mass balances to assess biogeochemical dynamics and its variability. [ABSTRACT FROM AUTHOR]