Trace elements of bivalve shells can potentially serve as proxies of environmental change. However, to reconstruct past environments using the geochemical properties of the shells and determine the degree to which the element levels are biologically influenced, it is essential to experimentally determine the relationship between environmental variables and the element composition of the shells. To disentangle possible controls on the incorporation of strontium and barium into freshwater bivalve shells, we conducted controlled laboratory experiments using the extremely salinity and temperature tolerant Asian clam, Corbicula fluminea as a model species. Bivalves were reared for five weeks in two sets of experiments: (1) combinations of different water temperature (10, 16 and 22 °C) and food levels (0.2, 2, 4 and 8 × 104 cells/ml) with constant Sr/Cawater (2.45 mmol/mol) and Ba/Cawater (367 μmol/mol) levels; and (2) combinations of different water temperature (10, 16 and 22 °C) and different Sr/Cawater (ca. 4, 8 and 12 mmol/mol) and Ba/Cawater levels (ca. 600, 1150 and 1500 μmol/mol) with constant food level (4 × 104 cells/ml). The Sr/Cashell ratio of C. fluminea exhibited a statistically significant negative correlation with temperature and a positive correlation to Sr/Cawater, but was not affected by changing food level or shell growth rate. On the contrary, Ba/Cashell was influenced by a complexly intertwined set of variables including temperature, food level, Ba/Cawater and shell growth rate. Partition coefficients of KDSr/Ca (0.19 to 0.29) and KDBa/Ca (0.03 to 0.19) confirmed the control of vital effects over strontium and barium incorporation into the shells. As indicated by the findings, Sr/Cashell of C. fluminea from freshwater environments can serve as a reliable proxy for past water temperature if the spatiotemporal variability of strontium-to-calcium in the water is small, well-known or can be estimated from other proxies. Interpreting Ba/Cashell values, however, is much more challenging because they are controlled by a large number of environmental and physiological variables. Sr/Cashell and Ba/Cashell of C. fluminea specimens from estuarine settings in which element-to-calcium ratios are more conservative and stable can potentially function as paleoenvironmental proxies. Findings of this study can be useful to better understand the element incorporation into shells of other bivalves including marine species.