Hypoxia (oxygen scarcity) is widespread in tropical freshwaters, particularly in dense swamps, and may be an important factor structuring benthic macroinvertebrate communities. Macroinvertebrates show a diversity of respiratory modes ranging from atmospheric breathing to tracheal gill breathing, and these adaptations affect their ability to use hypoxic water. The objectives of this study were to (a) describe the benthic macroinvertebrate community from ten swamp and river sites in Kibale National Park, Uganda, (b) determine the degree to which dissolved oxygen explains variation in abundance of respiratory groups (taxa with a similar respiratory mode) among sites, and (c) test for significant seasonal variation in the abundance of the numerically dominant respiratory groups. Macroinvertebrates from monthly collections over a two-year period were identified to the lowest taxonomic level necessary to place them in functional respiratory groups. Across all sites, both the relative and absolute abundance of atmospheric breathers (e.g., pulmonate snails and nepids) and mantle/ctenidia breathers (primarily fingernail clams) were negatively correlated with dissolved oxygen, while the abundance of tracheal gill breathers (e.g., anisopterans and zygopterans) was positively correlated with dissolved oxygen. We did not detect significant seasonal trends in catch per unit effort of numerically dominant respiratory groups. Dissolved oxygen concentration was a good predictor of the abundance of some respiratory groups and may be a key factor in maintaining the structure and diversity of these assemblages.