The purpose of this research is to provide a comprehensive assessment of the concentration levels and spatial variability of cadmium (Cd), copper (Cu), mercury (Hg), lead (Pb) and zinc (Zn) in El Tobari Lagoon in surface sediments during two seasons for several geochemical variables that could explain the observed heavy metal variability. Seventy-two surface sediments samples were collected in 12 different sites of the El Tobari Lagoon. Sediment samples were dried and subjected to acid extraction using a microwave system and five metals (Cd, Cu, Hg, Pb and Zn) were measured using atomic adsorption spectrometry. A certificate sediment material and blanks were used as quality control purposes. The enrichment factor (EF) and the index of geoaccumulation (Igeo) were calculated as index of metals contamination for the sediments, using aluminum as the conservative element. The five metals examined in sediments from El Tobari Lagoon exhibited a linear correlation with Al as result of the large specific surface areas of these sediment components and the chemical affinities between them. The metals contents in sites of the El Tobari Lagoon were variable, and Cd, Cu and Hg presented a seasonal behavior. The enrichment factor and index of geoaccumulation analysis indicated that Cd and Hg exhibited a certain extent (EF for Cd ranged from 4.10 to 10.29; EF for Hg ranged from 2.77 to 12.89) of anthropogenic pollution, while Cu showed sporadic (EF ranged from 0.43 to 2.54) anthropogenic contamination. The highest concentrations of Cd, Cu and Hg were found in the sites that regularly received discharge effluents from agriculture and aquaculture.