Ammonia emissions from swine waste lagoons pose an environmental challenge to current pork production practices.  Semi-permeable lagoon covers limit ammonia emissions by minimizing the effect of wind on the lagoon surface.  Additionally, 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 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).  Molecular analysis (PCR, DGGE, sequencing, and qPCR) of the amoA genes indicated that the community was dominated by ammonia oxidizing bacteria and not archaea.  Molecular and functional analysis of the semi-permeable cover material demonstrated that a nitrifying community was established and enriched in the cover material relative to the underlying lagoon water.