Ammonia emissions from swine waste lagoons pose an environmental challenge to current pork production practices. Semi-permeable lagoon covers can be used to limit ammonia emissions by minimizing the effect of wind on the lagoon surface. However, semi-permeable covers may also act as an attachment site for biofilm development, but microbial analysis of cover biofilm is needed to better assess this aspect of the technology. Samples of biofilm-encrusted mature cover and underlying lagoon wastewater liquids were collected from three swine waste sites, and their potential nitrifying and denitrifying activities were assessed relative to new cover material in laboratory experiments. Potential nitrification activity for the biofilm samples ranged from 0 to 1.6 mmoles nitrite m^-2 d^-1 during a 24-hour period. No nitrite accumulated in new cover (no biofilm) and negative control samples during the three experiments. Lagoon wastewater samples had limited nitrification potential and produced from 0 to 0.5 mmoles nitrite m^-2 d^-1 (5 L volume for comparison). Potential denitrifying activity (measured over 8 days) in biofilm samples consumed from 2.0 to 3.7 mmoles NO_x^- (nitrate + nitrite) m^-2 d^-1. No nitrate or nitrite was consumed in the new cover or negative control samples. Wastewater samples consumed from 0 to 2.9 mmoles NO_x^- m^-2 d^-1. It appears that the semi-permeable cover material served as a useful support for the growth of a beneficial biofilm community with the capacity to transform NH₃ to N₂ via a coupled nitrifying and denitrifying process.