Diatoms interact with aquatic environments in such a manner that their distribution determines how other organisms are distributed, e.g., bivalve mollusks who feed on them. The aim of this study was to determine if the diatom taxa filtered by Crassostrea corteziensis in the wild remained constant or changed due to substrate, site or season in which they grow. Thus, we tested the null hypothesis (H₀) that the species composition of diatoms filtered by oysters from different substrates, sites and seasons were to be similar. So, diatoms extracted from the digestive tract of oysters from different substrates, sites, and seasons were identified and quantified. Diatom structure was described based on ecological indices (H', N1, J', 1-λ). Similarity measured using the Bray-Curtis index, from which a PERMANOVA test was performed and graphed using non-metric multidimensional scaling (nMDS) and similarity profile (SIMPROF). Analyses indicated that diatom assemblages filtered by oysters varied by site and season, but not by substrate. The diatom assemblages defined by sites were characterized by Neodelphineis silenda, Thalassionema nitzchioides, Cymatotheca complex (C. weissflogii and C. minima), and Navicula sp. 5; while the diatom assemblages defined by seasons were characterized by N. silenda, Skeletonema costatum, Aulacoseira granulata, and A. granulata var. angustissima. Meanwhile, N. silenda, T. nitzschioides, and Cymatotheca complex remained constant throughout the substrates. The evidence generated allows us to conclude that C. corteziensis filtered on the same diatom assemblage regardless of the substrate in which it was found; however, these assemblages differed depending on the site and the season.