Biogenic carbonates, including bivalve shells, record past environmental conditions, but their interpretation requires understanding environmental and biological factors that affect trace metal uptake. We examined stable barium (δ138Ba) and radiogenic strontium (87Sr/86Sr) isotope ratios in the aragonite shells of four native freshwater mussel species and two invasive species in five streams and assessed the effects of species identity, growth rate, and river water chemistry on shell isotopic composition. Shells were robust proxies for Sr, accurately reflecting 87Sr/86Sr ratios of river water, regardless of species or growth rate. In contrast, shell δ138Ba values, apart from invasive Corbicula fluminea, departed widely from those of river water and varied according to species and growth rate. Apparent fractionation between river water and the shell (Δ138Bashell-water) reached -0.86‰, the greatest offset observed for carbonate minerals. The shell deposited during slow growth periods was more enriched in lighter Ba isotopes than the rapidly deposited shell; thus, this phenomenon cannot be explained by aragonite precipitation kinetics. Instead, biological ion transport processes linked to growth rate may be largely responsible for Ba isotope variation. Our results provide information necessary to interpret water chemistry records preserved in shells and provide insights into biomineralization processes and bivalve biochemistry.