The main goal of this monitoring program was to evaluate the contamination in the intertidal environment of Óbidos Lagoon by the metals Cd, Pb, and Ni on water, sediments, and on biological samples, using the bivalve Cerastoderma edule (common name: cockle) as a biomonitor. Since C. edule is an edible mollusc, the risk of their consumption by humans from this lagoon was also evaluated. The study was performed in a restricted area of the lagoon—the ML station—where human activities, such as shellfish harvesting, intersect with the natural processes occurring in this system. The results obtained revealed that the water samples were polluted with Cd and Pb with concentrations (0.00025 mg l⁻¹ and 0.0072 mg l⁻¹) above the maximum legislated on the Directive 2008/105/EC, while for Ni, this occurred only on one of the seasons sampled (summer 2010: 0.029 mg l⁻¹). The sediments were not contaminated with Cd and Ni, and the contamination detected for the metal Pb, allowed the classification of this station as an unpolluted site ([Pbmin] = 7.477 mg.kg⁻¹ and [Pbmax] = 19.875 mg.kg⁻¹). On biological samples, comparing the results of metal contaminations with the values of the maximum levels fixed by European Commission Regulation (EC) No 1881/2006 and USFDA, all the results were below the legal value. Therefore, during the period of study, the consumption of this bivalve by humans was safe. Also, BAF and CF calculations suggest that C. edule can be used as a biomonitor to determine the source of the contaminations. This study supported the use of C. edule as a biomonitor to assess the contamination by the metals Pb and Ni at the Óbidos Lagoon and allowed to predict the potential transfer of metals to higher trophic levels with potential impacts on the natural and human communities.