Reservoir sediment contamination with heavy metals produced by mining activities has aroused widespread global concern owing to its potential threat to human health. In this study, the total concentrations and speciation of heavy metals (Cd, Pb, Zn) in the Lexi (LX) and Maoshui (MS) reservoirs around the historical artisanal zinc smelting area in Southwest China were determined, and pollution indices were applied to assess the pollution levels and potential ecological risks of the two reservoirs. The results showed that all the detected samples in the two reservoirs presented significant metal accumulation, especially for Cd, as compared with the soil background values in Guizhou Province. Between the two reservoirs, the vertical distribution characteristics of each metal in sediment columns were similar. The heavy metal concentrations of the three columns in the LX reservoir reached their maxima at 35, 15, and 10 cm and showed a trend of first increasing and then decreasing overall. However, the heavy metal contents of the three columns in the MS reservoir all exhibited wave-like characteristics in the vertical direction, and all of them reached a relatively obvious high point at approximately 5 and 30 cm. The geoaccumulation index (I) and potential ecological risk index (RI) indicated that Cd was strongly enriched and represented the main risk factor, and the pollution level of the MS reservoir was significantly higher than that of the LX reservoir. Furthermore, the effect coefficients (ERMQ) confirmed that the two reservoirs are likely to have toxic impacts on aquatic organisms and need to be controlled and mitigated. The speciation analysis of heavy metals revealed that Cd was primarily in the acid-extractable fraction (69.57%, 68.28%), Pb was chiefly in the reducible fraction (55.24%, 42.18%) and oxidizable fraction (22.60%, 38.02%), and Zn was mainly in the oxidizable fraction (32.54%, 37.65%) in the LX and MS reservoirs, respectively. The ratios of the secondary phase and primary phase (RSP) and risk assessment code (RAC) evaluation demonstrated that Cd in the sediments of the two reservoirs presents a very high potential ecological risk, and Pb and Zn were at medium to high ecological risk levels. This study highlighted that the artisanal zinc smelting activities had caused serious heavy metal pollution in reservoir sediments, posing a threat to the local ecological environment.