Diatoms are well recognized as indicators of contamination by heavy metals whose effects may alter the structure of benthic diatom assemblages. The southern beaches of Bahía La Ventana, Baja California Sur, Mexico are supplied with sediments that are naturally or anthropogenically enriched with potentially toxic elements. Thus, we carried out a geochemical assessment for trace elements in the intertidal beach sediments and we measured diversity of benthic diatom assemblages found in the intertidal sediments and on subtidal rocks. Sampling was done in March, June and September 2012. Chemical analysis was performed using acid digestion using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) for determining the concentration of 17 elements, and their Normalized Enrichment Factor values were estimated. Low to moderately degrees of enrichment for Strontium (Sr), Antimony (Sb) and Barium (Ba) were detected. Diatom taxa were identified using optic microscopy. Diversity values (species richness, dominance and evenness) were calculated. Diatom assemblages showed a high species richness with 182 taxa (species and varieties), including 30 new records for the region and 14 for Mexican waters. These, together with the high estimated values of diversity (H', J', λ) characterize a typical assemblage of benthic marine diatoms.