<p>Understanding biodiversity patterns is crucial to guide management actions in coastal ecosystems. Alpha and beta diversity provide complementary insights into community dynamics and are essential for a comprehensive biodiversity assessment in dynamic coastal ecosystems like tidal flats, where environmental gradients shape the distribution patterns of benthic organisms. In this study, we compared the alpha and beta diversity of benthic molluscan assemblages along the environmental gradient (from outer to inner sites) within two tidal flats in the Marine Protected Area of San Antonio Bay (Patagonia, Argentina). Our results showed consistent diversity patterns and compositional shifts in molluscan assemblages from the outer to the innermost tidal flat sectors. Molluscan alpha diversity increased from impoverished inner sites to well-structured assemblages at outer sites, with notable differences in both spatial and temporal beta diversity. These assemblages’ dissimilarities, driven by differential contributions of turnover and nestedness, highlight different ecological dynamics across tidal flats and emphasize the need for specific studies to assess the role of environmental and anthropogenic factors that drive the diversity in the benthic molluscan assemblages of San Antonio Bay.</p>