The presence of antibiotic resistant bacteria in non-clinical environments is the result of multiple selective pressures and evolutionary processes. To test the hypothesis that metal exposure is one selective pressure maintaining antibiotic resistance in aquatic bacteria, both bacterial community tolerance to metals and antibiotics and the relative abundance of antibiotic and metal resistance determinants were quantified along a gradient of metal contamination in freshwater microbial microhabitats on the Savannah River Site (SRS), SC, and in experimental freshwater microcosms. Phenotypic resistance to metals and antibiotics, and resistance determinants were greatest in metal-exposed bacterial communities supporting the hypothesis. The relative abundance of mobile genetic elements called class 1 integrons were then compared in contaminated and reference freshwater and estuarine microhabitats, and in experimental microcosms, to test the hypothesis that elements involved in the acquisition of exogenous sources of DNA are more abundant in bacterial communities exposed to metal contaminants . The structure and predicted function of the integron-associated gene cassette pool was then compared using fragment analysis to assess how metal contamination shapes the gene cassette pool. Results indicate that class 1 integrons are abundant in environmental bacteria, and gene cassettes are a diverse genetic resource that can contribute to bacterial evolution. The complete nucleotide sequence of a 130 kb plasmid from a multidrug resistant Escherichia coli strain isolated from a contaminated estuary was determined to assess potential antibiotic resistance gene flow between clinical and environmental populations and the co-occurrence of metal and antibiotic resistance elements on the same plasmid. The plasmid contained several genes conferring resistance to multiple classes of antibiotics in a region with numerous insertion sequences, transposons, and integrons, yet no known metal resistance genes were identified. The sequence reveals that antibiotic resistance genes prevalent in clinically-derived isolates are prevalent in an environmental strain as well. The results of these studies indicate that antibiotic resistance persists in the environment, and that metal exposure selects for resistance phenotypes, genotypes, and genes involved in horizontal transfer.