This study provides the first numerical simulation of physical and biogeochemical processes in a very turbid and highly eutrophic tropical reservoir of the Trans-Mexican Volcanic Belt in Mexico. The Cointzio reservoir (capacity 66Mm3) is characterized by a lack of water treatment plants upstream and a high content of very fine clay particles. It suffers serious episodes of eutrophication associated with high levels of turbidity and benthic anoxia. Different scenarios for future climate inputs, nutrient inputs and water levels were simulated. The results pointed out the potential negative long-term impact of climate change on this reservoir. In this region, an increase of average air temperature as high as 4.4°C is expected by the end of the century. When coupled with a low water level, this increase could lead to critical conditions with a severe depletion of dissolved oxygen and important algal blooms with chlorophyll a reaching values of up to 94μgL−1. The calculations indicated that a drastic reduction of nutrient inputs (up to 90%) would be required to significantly reduce chlorophyll a concentrations. If such mitigation measures are adopted, the maximum peak of chlorophyll a would be reduced by 55% after a ten-year period of efforts, with corresponding positive effect on dissolved oxygen concentrations. The main limitation of the chosen numerical approach comes from the assumption of a constant water level in the model. This may be particularly critical for shallow type reservoirs.While this region remains poorly studied, this study brings original information that will help stakeholders to adopt appropriate strategies for the management of their waterbodies that experience critical eutrophication.