Nitrogen and phosphorous loading drives eutrophication of aquatic systems. Lakes and reservoirs are often effective N and P sinks, but information is needed on the variability of their biogeochemical dynamics, especially for tropical systems. A long-term N and P mass balance (2003-2018) in a small tropical eutrophic reservoir lake, Valle de Bravo (VB), Mexico, showed it is a net sink of N (-41.7 g N m-2 y-1), and P (-2.7 g P m-2 y-1), mainly 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). N mass balance showed that VB 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. During a period of high water level fluctuations (WLF), the net N atmospheric flux decreased by half compared to high level years. WLF can be a useful management tool to improve the trophic status of water bodies by decreasing anoxic conditions and net atmospheric fluxes, possibly through decreasing nitrogen fixation and/or promoting denitrification and other microbial processes that alleviate the N load.