It is a common practice in the midwestern United States to raise swine in buildings with under-floor slurry storage systems designed to store manure for up to one year. These so-called “deep-pit” systems are a concentrated source for the emissions of ammonia (NH3), hydrogen sulfide (H2S), and odors. As part of a larger six-state research effort (U.S. Department of Agriculture-Initiative for Future Agriculture and Food Systems Project, “Aerial Pollutant Emissions from Confined Animal Buildings”), real-time NH3 and H2S with incremental odor emission data were collected for two annual slurry removal events. For this study, two 1000-head deep-pit swine finishing facilities in central Iowa were monitored with one-year storage of slurry maintained in a 2.4 m-deep concrete pit (or holding tank) below the animal-occupied zone. Results show that the H2S emission, measured during four independent slurry removal events over two years, increased by an average of 61.9 times relative to the before-removal H2S emission levels. This increase persisted during the agitation process of the slurry that on average occurred over an 8-hr time period. At the conclusion of slurry agitation, the H2S emission decreased by an average of 10.4 times the before-removal emission level. NH3 emission during agitation increased by an average of 4.6 times the before-removal emission level and increased by an average of 1.5 times the before-removal emission level after slurry removal was completed. Odor emission increased by a factor of 3.4 times the before-removal odor emission level and decreased after the slurry-removal event by a factor of 5.6 times the before-removal emission level. The results indicate that maintaining an adequate barn ventilation rate regardless of animal comfort demand is essential to keeping gas levels inside the barn below hazardous levels.