The total and bioavailable contents of Co, Cr, Cu, Fe, Mn, Ni, Pb and Zn in surface sediments from 77 sites in the Altata-Ensenada del Pabellón (AEP) lagoon complex were determined by Atomic Absorption Spectrometry, after inverted aqua regia (HNO3/HCl 3:1) and sodium acetate 1M (adjusting pH = 5 with acetic acid) digestion, respectively. The ratio between the bioavailable fraction and the total concentration (BAP: BioAvailable Proportion), for each metal, was examined according to the chemical parameters of the bottom waters (dissolved oxygen and salinity) and geochemical characteristics of the sediments (organic carbon and total Al, Fe and Mn contents). Highest bioavailable concentrations of metals were associated with agricultural discharges and Culiacán River inputs. According to the Canadian Sediment Quality Guidelines, the Pb bioavailable content can produce adverse effects on organisms. Total concentration of Cu, Mn, Pb and Zn played an important role in the fractioning of these metals. Organic carbon, fine sediment, Fe and Mn hydroxides and aluminosilicates influenced the behaviour of Cu, Fe Ni and Zn BAP's.