Molluscs are a diverse phylum in coastal lagoons because the numerous taxa collectively display broad ranges of optima and tolerance with respect to ambient conditions. We report on the taxonomic composition, habitat preferences and feeding guilds of molluscs from Río Lagartos coastal lagoon, Mexico. Molluscs were collected in the rainy season (September/October 2017), during the winter (Nortes) season (February 2018) and at the end of the warm, dry season (May 2018). Samples were taken using a Ponar dredge, a cylindrical PVC core barrel, or a beach seine. We studied the abiotic characteristics (sediment grain-size distributions, submersed aquatic vegetation abundance and salinity) to explore assemblage differences across the broad salinity gradient that characterizes the system (~30–78 PSU). Molluscs were represented by 39 species, 34 genera, 23 families and two classes. Stenohaline species were more numerous overall than euryhaline species, but their occurrence in samples was low (<20% of the samples). Stenohaline taxa lived primarily in environments characterized by marine salinity, and few were found under hypersaline conditions. We collected a smaller number of species than did studies carried out in the lagoon >35 years ago. Species accumulation curves revealed that the full species richness was not captured in our study. Euhaline environments displayed greater mollusc species richness and had a larger proportion of amount (mass) of submersed aquatic vegetation. In the hypersaline environments, species richness may be favoured by the lower dominance of sands. Suspension feeders were the most diverse group in both the euhaline and hyperhaline environments.