A reservoir with ecological and economic importance and its major tributary, localized in east-central Mexico, were studied. The aim of this work was to know the physicochemical water characteristics of both water bodies and to contrast these by their different uses, and also estimate overall water quality using a Water Quality Index (WQI). Water samples from the reservoir and the tributary were obtained in different climatic seasons. In the tributary, anoxic and hypoxic conditions and high levels of organic matter, orthophosphate, and ammonium showed that this is strongly impacted by wastewater discharges and that the water is not suitable for different uses; independently of the season, the WQI showed “poor” quality (34.4–47.2). In contrast, in the reservoir a better water quality was determined; the WQI in the sampling months ranged from 72.1–76.6 (“good” quality), and spatially, this was from 66.5–79.5 (“fair” and “good” quality).