The squalid callista clam (Megapitaria squalida) is a popular raw seafood item for human consumption; however, as a filter feeder, this clam accumulates heavy metals from natural and anthropogenic sources. The concentrations of copper (Cu), cadmium (Cd), chromium (Cr), nickel (Ni), lead (Pb), zinc (Zn), arsenic (As), and mercury (Hg) in sediments and the soft tissues of M. squalida from two sites on the southeastern coast of the Gulf of California, Mexico, were evaluated from April 2016 to April 2017 on a monthly basis. The metal concentrations in sediments from both sites did not exceed the Mexican and international regulations. Concentrations of Cd and Pb in the clams from Altata bay (2.49 and 5.68 µg/g dw, respectively) and Agiabampo bay (2.38 and 5.54 µg/g dw, respectively) exceeded the permissible limits recommended by Mexican sanitary regulations, thus representing a threat to human health. The higher values of Cd, As, and Hg obtained for the biota sediment accumulation factor in both sampling areas indicate that squalid callista is a strong accumulator of these metals. The metal burdens in sediments and M. squalida soft tissues are influenced by chemicals from agriculture and aquaculture, as well as urban sewage disposal near both sites. This study brings useful information on metal bioaccumulation in one of the most important commercial clam species on the Pacific coast.