Rapid urbanization and the absence of efficient water management policies are increasingly degrading the water quality of tropical reservoirs in developing countries. The small tropical reservoir of Cointzio, located in the Trans-Mexican Volcanic Belt, is a warm monomictic water body (surface area = 6 km2 with short water residence time <1 year) that is strategic to the drinking water supply of the city of Morelia and to downstream irrigation during the dry season (6 months of the year). The reservoir faces two threats: (a) reduced water storage capacity due to sediment accumulation and (b) eutrophication caused by excess nutrients that likely come from untreated wastewaters in the upstream watershed. Intensive field measurements of water and sediment were conducted in 2009 to characterize the trophic status of the reservoir and to estimate nitrogen (N) and phosphorus (P) sources, total suspended sediment (TSS) (N), (P), and carbon (C) loads, and their accumulation or removal in the reservoir. We found that point sources represent the majority of N and P inputs to the reservoir. The trophic status is clearly eutrophic given the high chlorophyll a peaks (up to 70 µg L−1) and a long period of anoxia (from May to October). Most of the TSS, C, N, and P were conveyed to the reservoir between June and October during the wet season. The TSS yield from the watershed was estimated at 35 ± 19 t km−2 year−1, of which more than 90 % was trapped in the reservoir (sediment accumulation rate = 7800 ± 2100 g m−2 of reservoir year−1). The export load of C, N, and P downstream at the reservoir outlet was reduced by 31, 46 and 30 % respectively in comparison to the load at the reservoir inlet. This study reveals the effect of climatic seasonality on inputs to tropical reservoirs and accumulation; it also highlights the need to both reduce nutrient input to combat eutrophication and mitigate erosion to maintain the water storage capacity of the reservoir over the long term.