Anthropic eutrophication is one of the most widespread problems affecting water quality worldwide. This condition is caused by excessive nutrient inputs to aquatic systems, and one of the main consequences is accelerated phytoplankton growth. Eutrophication can lead to damage to human health, the environment, society, and the economy. One of the most serious consequences of eutrophication is the proliferation of cyanobacteria that can release toxins into the water. The aim of this research was to evaluate the trophic condition of a tropical reservoir over the course of time, using a database extending over 15 years to investigate relationships with environmental conditions, considering spatial heterogeneity and seasonality, as well as inter-relations between trophic state indicators. Data for chlorophyll-a, total phosphorus, and total nitrogen were collected from 2000 to 2014, and cyanobacteria abundance was determined from 2004 to 2014. The trophic state index was also calculated. The results demonstrated the existence of two distinct compartments in the reservoir: one lotic and the other lentic. No relationship was observed between chlorophyll-a and phosphorus. The results suggested that phytoplankton growth was mainly controlled by nitrogen concentrations. These conditions favored cyanobacteria predominance, resulting in increasing abundance of these potentially toxic bacteria over time. The model obtained indicated hypereutrophic conditions, with high phytoplankton biomass and cyanobacteria abundance during the next years likely to affect the uses of the water of the reservoir.