Few studies have examined the influence of reservoir hydrodynamics on the water quality of its limnological zones. In this study, the relationships between the operational phases and the water quality of the limnological zones were assessed for the Amazonian reservoir Tucuruí. Limnological zones were clustered by means of an artificial neural network technique, and inputs used were water quality variables, measured at twelve stations between 2006 and 2016. Generalized Linear Models (GLMs) were then used to identify the influence of the operational phases of the reservoir on the water quality of its limnological zones. The GLM with a gamma-distributed response variable indicated that Chlorophyll-a concentrations in the riverine and transitional zones differed notably from those observed in the lacustrine zone. Chlorophyll-a concentrations were significantly lower during the operational falling water phase than in the low water phase (p < 0.05). The GLM with an inverse Gaussian-distributed response variable indicated that Secchi depth was significantly lower in the riverine than in the lacustrine limnological zone (p < 0.05). Our results suggest that more eutrophic conditions occur during the operational rising water phase, and that the area most vulnerable to eutrophication is the transitional zone. We demonstrate that the use of GLMs is suitable for determining areas and operational phases most vulnerable to eutrophication. We envisage that this information will be useful to decision-makers when monitoring the water quality of hydroelectric reservoirs with dendritic patterns and dynamic operational phases.