Description: Amino acids were isolated from the muscle tissue of Corbicula fluminea and Potamocorbula amurensis; two co-occurring invasive clams within the San Francisco Bay-Delta system. Clam specimens were collected near Montezuma Slough (Contra Costa County, California) at the confluence of the Sacramento and San Joaquin Rivers twice during the hydrological extremes of 2010 water year (November, 2009 and May, 2010). Carbon and nitrogen isotope values of individual amino acids were measured. Clam specimens were collected at USGS Sites 2.1 and processed following Stewart et al. (2013; doi:10.3354/meps10503). Amino acids were hydrolyzed from clam muscle tissue, derivatized, and isolated following Vokhshoori et al. (2013; doi:10.3354/meps10746). The measurement of the carbon and nitrogen isotope values of individual amino acids were conducted following Vokhshoori et al., 2013 and Vokhshoori and McCarthy, 2013 (doi:10.1371/journal.pone.0098087), respectively. The purpose of this study was to monitor biogeochemistry during 2010 water year and assess dietary difference between two co-occurring invasive species. This study focused on two species, C. fluminea and P. amurensis, benthic sessile primary consumers that can inhabit the same environment. USGS Site 2.1 was specifically selected as it exhibited the environmental conditions where both clam species co-existed during 2010 water year. This design allowed for interspecies variation to be explored. Nitrogen isotopes of amino acids were used to isolate variations in nutrient baseline from dietary changes across the season between the two species. Carbon isotopes of amino acid were utilized to understand the diet of the two species at two points in the season.