Freshwater mussel populations are highly susceptible to environmental alterations because of their diminished numbers and primarily sessile behaviors; nonlethal biomonitoring programs are needed to evaluate the health of populations prior to mass mortality events. Our objectives were to determine (i) which biochemical parameters in freshwater mussel hemolymph could be consistently quantified, (ii) how hemolymph parameters and tissue glycogen respond to a thermal stress gradient (25, 30, and 35 °C), and (iii) the effects of tissue and hemolymph extraction on long-term growth and survival of smaller- and larger-bodied mussel species. Glucose exhibited elevated expression in both species with increasing water temperature. Two transaminase enzymes had elevated expression in the 30 °C treatment. The effects of hemolymph extraction and tissue biopsies were evaluated with a large-bodied species, Elliptio crassidens, and a smaller species, Villosa vibex. Individuals were monitored for 820 to 945 days after one of four treatments: hemolymph extraction, tissue biopsy, tissue and hemolymph extraction, and control. Hemolymph extraction and tissue biopsy adversely affected survival of V. vibex, suggesting that these extraction methods may add some risk of reduced survival to smaller-bodied species. Survival of E. crassidens was not impaired by any of the treatments, supporting the use of these techniques in nonlethal biomonitoring programs for larger-bodied mussel species.