The José Antonio Alzate Dam in the State of Mexico, Mexico, receives wastewaters from domestic, industrial, and agricultural activities through the Lerma River. Chemical and physicochemical characteristics of the water were determined. Sediment has been studied in order to define the importance of its influence on the reservoir's state as a whole. The quantification of the metals, Cd, Cu, and Pb in total forms and the geochemical distribution and the chemical mobility of these metals in sediment have been established using a chemical sequential extraction scheme. The three metals showed a common characteristic, being more abundant in fraction F6 (residual), but the other fractions of the geochemical distribution were variable depending on the metal. First, the contamination level was evaluated with the results of the total metals, using the criteria of EPA, Thomas and Murdoch, and the Ontario Ministry of Environment for sediment in water bodies. Subsequently, the risk was assessed using the same criteria but considering the results of sequential extractions, where the geochemical distribution of each metal allowed a better understanding of metal portions with more influence on the risk, in which Cu and Pb presented low risk, but not Cd.