Human activities, such as the release of pollutants, have exerted profound effects on the environment and on organisms in recent geologic years. Aquatic pollutants, such as mercury (Hg), can remain in a water body for prolonged periods of time. The chronic exposure of Hg to aquatic organisms can lead to a reduction in effective population sizes through the selection of tolerant genotypes, bottleneck events and pollutants acting as a barrier to gene flow. Organisms are exposed to Hg through the ingestion of food and through the water-column. However, first, the bioaccumulative form of Hg, monomethylmercury (MeHg), must be available for accumulation. MeHg exposure can induce alterations in gene expression levels in aquatic organisms, such as fish, that allow for the detoxification and the breakdown of MeHg. Here, we evaluated the main sources of MeHg exposure to Rhinichthys atratulus (Eastern Blacknose Dace) and analyzed the genetics of R. atratulus that live in a historically Hg polluted watershed, the Still River watershed, CT. We studied four historically polluted sites (i.e. legacy sites) in the Still River basin that previously received direct point source Hg pollution from hat-making factories located nearby the Still River and its various tributaries. We compared legacy polluted sites to three reference sites with no known Hg point source pollution or any other form of point source chemical pollution. Our overall goals were to: i) determine the main environmental and biological drivers of MeHg exposure to R. atratulus living in the Still River watershed; and ii) identify the genetic diversity and the gene expression of R. atratulus living in a Hg polluted environment. We addressed the environmental and biological goal by investigating the MeHg accumulated in the sediment, water-column, food sources, and fish at each study site. We determined if there was a correlation between the MeHg levels found in the environment or food sources and MeHg accumulated in fish. Additionally, we determined if trophic dynamics influenced MeHg concentrations of fish by using stable nitrogen and carbon isotopes to project the trophic position fish were feeding at from the different study sites. We assessed the impact of chronic Hg exposure on the genetic diversity of fish by using microsatellites. We aimed to identify if there was any evidence of genetic erosion in the legacy populations compared to reference sites due to past Hg exposure. We also determined how gene flow shapes the genetic structure of fish at study sites. Lastly, we delved into the extent aqueous MeHg (wMeHg) exposure altered the gene expression in two populations. We compared fish from two sites with the highest and lowest levels of MeHg accumulated in their body. These two sites also significantly differed for their concentration of MeHg found in the water-column. We used quantitative polymerase chain reaction (qPCR) to focus on four genes that are involved in either reproduction, metal metabolism, oxidative stress, or apoptosis. We found that there were high concentrations of Hg in the environment at most legacy sites, but the environmental concentrations did not correlate with fish MeHg levels. Fish from two reference sites had the highest MeHg concentrations that appeared to be driven by the percent MeHg accumulated in fish food sources. We additionally found that four other sites have fish with elevated levels of MeHg that exceeded the concentrations of MeHg that the EPA suggests humans should ingest per week. Fish from legacy sites had similar, higher, or lower genetic diversity compared to reference sites based on the method in which genetic diversity was compared. There were low rates of gene flow among all sites, and all sites were found to be significantly different for their allelic structure. Fish from the two study sites showed differential gene expression mainly for genes involved in metal detoxification (Mt2), cell apoptosis (cjun), and potentially oxidative stress (Hsp70). Increased levels of expression were expected for these genes when experimental groups were exposed to elevated wMeHg concentrations. We found slight evidence for sites exposed to elevated wMeHg concentrations to have higher expression of cjun and Hsp70. Mt2 was surprisingly downregulated by populations exposed to high concentrations of wMeHg. More research needs to be conducted to determine the role Mt2 plays in the detoxification process, as its function is still debated. Overall, we are the first to conduct a comprehensive study on the historic mercury cycling in the Still River basin, CT, USA. Our study provides critical data on the route of Hg exposure to organisms and shows evidence of high levels of MeHg accumulated by fish living in this fluvial system. Our findings call for implementation of conservation and management actions for the Still River watershed to protect fish, wildlife, and humans from being exposed to the potent neurotoxin, MeHg.