We studied 127 samples of bivalve mollusks (Mediterranean mussel, Mytilus galloprovincialis; smooth clam, Callista chione; grooved carpet‐shell clam, Tapes decussatus; and striped venus clam, Chamelea gallina) obtained in the winter and spring of 2009 from retail fish and shellfish vendors in Granada, Spain. Samples were analyzed (raw and after steaming) to determine the prevalence of Escherichia coli, mesophilic aerobes, Staphylococcus aureus and the disease‐causing microorganisms Salmonella spp., Listeria monocytogenes and Vibrio parahaemolyticus. E. coli was found in 25% of raw samples and 4% of cooked samples. Aerobes were found in 89% of raw samples (more than 1,000 cfu/g), and S. aureus was found in 37.0%. Only one raw sample was positive for V. parahaemolyticus. The percentage of positive findings was fourfold as high in the spring sample as in the winter sample. Contamination was most frequent in the smooth clam, and samples obtained on Mondays were more frequently contaminated than those obtained on other days of the week. PRACTICAL APPLICATIONS Current Spanish legislation establishes that all bivalve mollusks intended for commercial sale and human consumption must be treated at a detoxification center. The application of detoxification is of fundamental importance because it constitutes a barrier against the transmission of bacterial and viral diseases of aquatic origin. We analyzed possible differences in contamination parameters in this type of shellfish, indicated characteristics that may be affected by alterations in quality, and discussed the potential effects of these alterations on human health.