Like many native endemic desert freshwater fish species, the June Sucker (Chasmistes liorus) is currently listed as endangered. Managers have increasingly turned to habitat restoration as a key component to recovery plans. For endangered species, one of the primary outcomes of habitat restoration is that it should result in successful reproduction and recruitment of individuals into the adult population. Confirmation of natural recruitment as a function of habitat restoration can only be achieved by establishing natal origins. Recent research has proven the validity of otolith microchemistry, a technique that analyzes small quantities of elements, to trace potamodromous fish to their natal tributaries. Previous studies have documented that localized habitats in terms of microchemistry are reflected in otolith composition, thereby potentially making this a valuable way of determining fish origins. The primary goal of this study is to use otolith microchemistry to establish natal origins of June Sucker, ultimately in order to evaluate whether tributary habitat restoration results in natural recruitment. To accomplish this I first determined if the water chemistry among the three main spawning tributaries differed from one another. Second, I determined if the otolith chemistry reflected the otolith chemistry. Lastly, I developed a statistical model capable of classifying fish to their respective tributary based the element:calcium ratios in the otolith microchemistry. Water chemistry differed significantly among all three spawning tributaries, and I observed a strong and significant relationship between otolith chemistry and water chemistry. The classification models based on otolith element:Ca signatures were capable of accurately classifying individual fish to their natal tributary (classification tree 89% accuracy; random forest model 91% accuracy), increasing the ability to determine if the fish’s origin is wild vs. hatchery. The data obtained from this study will advance the current understanding of the June sucker recruitment dynamics and result in a fundamental improvement in our ability to determine where natural recruitment into the adult spawning population is occurring. In addition, this knowledge may help evaluate factors limiting recruitment in Utah Lake tributaries, identify future restoration localities, and assist effectiveness monitoring of spawning habitat restoration efforts.