1. Overexploitation of freshwater resources coupled with climate change can affect the flow and temperature regimes in rivers, which can be catastrophic for aquatic biota. The San Saba and Llano rivers, located in central Texas, are experiencing low flows and stream dewatering owing to over-allocation. Both systems harbour imperilled species, including Lampsilis bracteata, Texas fatmucket, which has been proposed for listing under the US Endangered Species Act. It is suspected that elevated water temperatures are a contributing factor in its decline.2. The upper thermal tolerances of glochidia and juvenile life stages were evaluated within each river. Mussels were acclimated to 27 C and tested across a range of temperatures (30-39 C) in 24 h (glochidia) and 96 h (juveniles) laboratory tests.The resulting tolerances were related to in situ water temperature and discharge using a uniform continuous above-threshold analysis.3. In the Llano, the 24 h LT50 (lethal temperature resulting in 50% mortality) was 31.8 C (95% CI 31.5-32.1 C), whereas the 96 h LT50 was 32.4 C (95% CI 32.1-32.7 C). In the San Saba, the 24 h LT50 was 34.7 C (95% CI 34.5-35.0 C), whereas the 96 h LT50 was 32.5 C (95% CI 32.2-32.9 C). LT50 thresholds were not exceeded for L. bracteata within the San Saba, but LT05 (lethal temperature resulting in 5% mortality) thresholds were exceeded. Water temperature loggers were lost in the Llano River as a result of a large flood; however, samples reported by the Texas Commission on Environmental Quality show that the LT05 and LT50 for both glochidia and juveniles were exceeded.4. Findings from this study indicate that thermal tolerances of L. bracteata vary by population and that low flows may be contributing to its decline. Our approach is non-species and region specific, which means that the methods presented should help managers and conservationists evaluate whether reduced water quantity and elevated temperatures are exerting impacts on aquatic species within their region.