Risk interpretation and regulatory criteria to manage selenium risks to aquatic organisms are often based on fish-tissue concentrations. Because selenium toxicity in early-life stage fish is thought to stem from maternal transfer to embryos, selenium levels in egg and ovary tissues are considered the most relevant indicator of risk to fish populations. However, establishing a regulatory water-quality criterion expressed as a chemical concentration in fish egg and ovary tissues poses practical problems for monitoring. Capturing gravid fish may be difficult, particularly for species that leave the water body under assessment to spawn in tributaries. Small-bodied fish such as sculpin may be more readily catchable, but laboratory protocols may not accommodate analysis of small-mass tissues. The USEPA’s aquatic life criterion for selenium document includes extensive analyses and assumptions for relating selenium concentrations in egg and ovary tissues to concentrations in whole-body or muscle fillet tissues, which may be easier to obtain. In the Kootenai River basin (Idaho and Montana, USA), we have extensively sampled fish tissues to examine selenium concentration patterns across different species, seasons, and water concentrations from 2019 to 2024. We compare concentrations in ovary, liver, muscle, and reconstructed whole-body tissues for many species, including Prosopium williamsoni (Mountain Whitefish), Oncorynchus mykiss (Rainbow Trout), Richardsonius balteatus (Redside Shiner), Cottus cognatus (Slimy Sculpin), and Ptychocheilus oregonensis (Northern Pikeminnow). Our robust paired sampling datasets allow us to explore selenium in these fish tissues throughout the spawning cycle, comparing observed concentrations to reproductive factors such as egg development stage (assessed visually or via histology), gonadosomatic index (GSI), and collection date. We observed positive correlations between liver and muscle selenium concentrations and ovary selenium concentrations within the same individual fish, though the strength of the relationship varied by species. Some species exhibited significant negative correlations between selenium concentrations in ovary, muscle, or liver tissues and GSI. Results from this study will inform how tissue relations of selenium in Kootenai River fish compare to the relation outlined in the USEPA criterion, particularly regarding the suitability of muscle or whole-body concentrations as surrogates for egg and ovary concentrations.