Cuitzeo Lake is one of the largest and most important lakes in Mexico. It receives different types of pollutants through its main tributary, the Grande River of Morelia. The aim of this work was to determine if high concentrations of iron, zinc, and arsenic are present in sediments in an area near the river mouth to the lake, as well as to estimate the partitioning of these metals using a sequential extraction procedure in order to obtain information of their potential bioavailability. Sediment samples were collected from three different sites in Cuitzeo Lake and two sites in Grande River in both dry and wet seasons. A sequential extraction procedure was carried out to determine the concentrations of these elements in different geochemical phases of the sediments. Total metal concentrations were evaluated by using the enrichment factor and the geoaccumulation index. A comparison with sediment quality guidelines and shale values has also been made. The results indicate that sediments are considered unpolluted by iron and moderately polluted by zinc and arsenic. However, fractionation studies showed that significant amounts of Zn and As could be released to the lake ecosystem depending on the environmental conditions, representing a medium risk potential of bioavailability to the biota.