The Colorado River no longer reaches the Gulf of California in most years due to numerous upstream dams and associated water diversions for consumptive use. The downstream estuary in Mexico has undergone habitat change as a consequence; however, a paucity of pre-impact data has made it challenging to assess the full scope of change. Fortunately, along the shoreline in the estuary there are accumulations of clam and snail shells that predate dam construction and can provide an invaluable perspective on past community dynamics in the molluscan community. Shell accumulations in the estuary were sampled during 2013 and 2014 at three sites along the north-south salinity gradient that existed prior to upstream water diversions. The living community was sampled during 2014 at the northern-most of these sites, which corresponds to the most estuarine environment from the past. In the following five chapters, a variety of analytical methods are applied to different subsets of the samples to assess change at multiple levels of the ecological hierarchy. Major results from these chapters include: (1) identification of a new predatory snail species in the estuary; (2) evidence suggesting decreases in predator populations in the estuary due to reduction in prey availability; (3) documentation of population decreases in species with preferences for low-salinity conditions and population increases for species with preferences for high-salinity conditions; (4) increases in community evenness and richness in the post-impact community; (5) evidence suggesting a shift in the processes controlling community assembly from environmental preference and dispersal capacity to competition-colonization tradeoff; and, (6) a reduction in carbon emissions from the estuary due to decreases in the clam population. Restoration efforts are ongoing in the Colorado River estuary under multiple binational agreements between the United States and Mexico. The results presented here represent baseline data that can be used to evaluate the success of those efforts and to inform the best strategies for restoration success. Counterintuitive as it may seem, restoration success likely means a reduction in the number of species living in the estuary and an increase in estuarine carbon emissions.