To evaluate the total mercury accumulation (THg) in the Descoberto river basin environmental protection area (DREPA), nine sediment and water samples were collected from the Descoberto reservoir (lentic environment), and 23 in its tributaries (lotic environment), which are located in a densely urbanized area within the Descoberto river watershed, Brazil. The following physicochemical parameters of water were determined: dissolved oxygen (DO); hydrogen potential (pH); total dissolved solids (TDS); nitrate (NO3−); chloride (Cl−); temperature (T); sulfate (SO42−), and in sediment, the concentration of total mercury (THg) and volatile material (VM) was determined. THg concentrations in sediments showed a significant difference (p = 0.002) between tributaries (0.03 µg g−1 ± 0.02) and reservoir (0.08 µg g−1 ± 0.04), indicating accumulation in the lentic environment. Most of the results evaluated for ecotoxicological risks presented values below the concentration, at which adverse effects would rarely be observed, ERL (effects range low). However, in relation to the enrichment factor (EF), applied to identify the anthropogenic contribution, the results indicate that most of the samples are moderately polluted through atmospheric deposition due to vehicular traffic and agriculture. These results show that the likelihood of methylation in the lentic environment is higher than in the lotic environment.