Understanding how anthropogenic activity impacts the health and viability of wildlife populations is one of the most important tasks of environmental biology. A key concern related to bi-products of human activity is the accumulation of environmental pollutants within aquatic environments. Pollutants such as endocrine disruptors and heavy metals have the potential to impact both human and wildlife populations in contaminated areas. While much research has focused on how these compounds impact natural selection processes, such as viability and reproduction, their effect on sexual selection processes is not as clear. The goal of this dissertation was to address how environmental contaminants impact sexual selection processes in a sex-role reversed pipefish and evaluate how these effects may impact long-term population viability. Here we show that short periods of exposure to environmentally relevant concentrations of a synthetic estrogen result in male pipefish with female-like secondary sexual traits. While these males are capable of reproduction, exposed males are discriminated against by females in mate choice tests. In natural populations, this type of discrimination could reduce male mating opportunities, potentially reducing their reproductive success. In an additional component of this dissertation, it was discovered that pipefish populations around Mobile Bay, specifically Weeks Bay, are currently being exposed to significantly elevated levels of mercury. These populations are genetically distinct from coastal populations but moderate levels of gene flow occur among sites, and gene flow between contaminated and non-contaminated population may be influencing how environmental contaminants are impacting genetic diversity and population viability. In the case of endocrine disruptors, migration between contaminated and non-contaminated sites may negatively impact population viability. Morphological traits induced with exposure to contaminants may be maintained for extended periods of time, therefore, the effect the exposed phenotype has on mating dynamics and sexual selection could be carried to non-contaminated sites if exposed individuals move to new populations. On the other hand, immigration of individuals from non-contaminated sites into contaminated areas may help maintain genetic diversity within exposed populations. In conclusion, the work presented in this dissertation shows that the presence of environmental toxins can significantly impact sexual selection processes, which in turn can have profound effects on the viability and future evolutionary trajectory of populations. Future work in this area should not only address how these toxins impact individual fitness, but should also address how population structure may be influencing the severity of these compounds on natural populations.