These data were used to examine the effectiveness of a non-lethal tool (Bioelectrical Impedance Analysis, "BIA") to estimate the physiological condition of endangered and threatened fishes in the Colorado River Basin. We conducted laboratory trials using hatchery-raised Humpback Chub and Bonytail and wild-captured Roundtail Chub, where fish were subjected to different feeding trials to elucidate a response in physiological condition and different temperature treatments to approximate field conditions. At the end of each 6-week trial fish were removed from tanks, lateral and dorsal measurements of BIA were taken, and fish were sacrificed for proximate composition analysis (lipid, protein, water, ash, dry mass, energy density). We developed models that evaluated the effectiveness of BIA alone vs. standard morphological condition-based measurements taken in the field (e.g., using total length and wet mass). We conducted a simulation experiment to increase the observation error around morphological wet mass measurements to determine the crititcal error at which BIA becomes a more important predictor of proximate composition than condition factor. In addition, we tested the influence of different BIA temperature conversion factors (20 °C, 15 °C, none) for use in Humpback Chub GLMM models. We also conducted an experiment to determine mortality rates when standard field methods or BIA is used to estimate fish condition. Detailed methods and results are reported in the manuscript associated with this data publication.