Dam construction and water diversions along the Colorado River during the twentieth century have altered the downstream estuarine ecosystem. Although it is clear that the ecosystem has changed, a lack of pre-impact studies has made it challenging to determine the magnitude and direction of change. By using a paleontological approach, we can retrospectively estimate ecological conditions in the estuary from before dam construction, particularly for benthic organisms with preservable hard parts, such as the shells of bivalve mollusks. Here, for the first time, we quantify differences in evenness, richness, taxonomic similarity, and rank-order abundance between the bivalve community living in the estuary today and two potential geohistorical baselines, the accumulated dead shells on the tidal flat and an older accumulation – known to pre-date dam construction on the river – in nearby shell-rich beach ridges called cheniers.Analysis of more than 12,000 live and dead bivalves distributed among 18 species collected from the tidal flat and cheniers on Isla Montague – an island at the mouth of the Colorado River – indicates that the pre-dam bivalve community was dominated by Mulinia modesta and was characterized by low rarified species richness and evenness (indexed by Hurlbert’s Probability of Interspecific Encounter). The increase in these metrics in the live relative to the chenier assemblage reflects a shift in the estuary from brackish to full marine conditions after damming and water diversions reduced freshwater flow to the estuary during the twentieth century. The tidal flat death assemblage was more similar to the live assemblage, which suggests that it represents post-dam construction conditions due to a large input of recent shells, whereas the chenier assemblage is an appropriate pre-impact baseline. Taxonomic similarity and rank-order abundance, indexed by Jaccard-Chao and Spearman’s Rho metrics, respectively, were too conservative to detect these differences.These baseline data, most notably the documented changes between the live and chenier assemblages, can be used to assess the efficacy of restoration efforts in the estuary, such as the Minute 319 environmental pulse flows. If restoration efforts stimulate a response in the bivalve community, metric values for evenness and richness are expected to decrease and become more similar to those we report here for the pre-impact chenier assemblage.