Swine (Sus scrofa Linnaeus) are an invasive species with a negative impact on native terrestrial plant and animal diversity. Further, in its native range, excessive population size has been perceived as a potential problem. The effects of swine on aquatic organisms remain poorly documented. We investigated the effect of an unmanaged population of feral and free ranging swine upon aquatic habitat, invertebrates and microbes in a coastal plain stream in Louisiana. Sampling was conducted twice yearly, spring and fall, from August 2002 through April 2004, at five sites within the Mill Creek watershed. We measured stream characteristics, carbon and nitrogen, biochemical oxygen demand, fecal coliform counts and heterotrophic plate counts. We collected invertebrates from woody debris, microbes from the water column and identified both to the lowest practical taxon. Invertebrate, microbial, habitat and swine relationships were assessed with detrended and canonical correspondence analysis. Swine activity did not appear to alter stream habitats. However, swine changed the microbial taxonomic composition in the stream increasing pathogens. Swine also appeared to have a positive relationship with gastropods (snails) and a negative relationship with collecting and scraping (predominantly insect) taxa in the streams. We suggest the decline of scraper taxa may be related to the changes in microbial composition. Shifts in the invertebrate community can impact other organisms in the ecosystem, and the full extent of swine impacts on other aquatic organisms may also be negative.