Standard metabolic rates (SMR) were measured empirically for carmine shiner Notropis percobromus and common shiner Luxilus cornutus to develop SMR models that predict metabolic responses of each species under thermal conditions observed in the wild. SMR increased significantly with body mass and rising water temperature, ranging from 0.05 mg O2 h−1 at 10°C to 0.89 mg O2 h−1 at 20°C for N. percobromus weighing 0.6–2.5 g and from 0.11 mg O2 h−1 at 10°C to 0.98 mg O2 h−1 at 20°C for L. cornutus weighing 0.8–6.6 g. SMR models significantly differed between sympatric species on account of differences in model intercepts (RA) and temperature coefficients (RQ), however, the allometric relationships between mass and SMR did not significantly differ between species. Known distribution of N. percobromus and L. cornutus includes the Birch River located in Manitoba, Canada, where N. percobromus is listed as Endangered. Little is known about the physiology of N. percobromus or the species' ability to acclimate or adapt to different environmental conditions. While size differences between species contributed, in part, to differences in SMR predictions for Birch River populations, SMR trends (< 2 mg O2 h−1) for individuals weighing 1 g were similar for both species across daily temperatures. Respirometry experiments contributed to developing species‐specific SMR models and inform on the effect of natural and anthropogenic stressors, namely water temperature, on the conservation of N. percobromus in this ecosystem.