Macroinvertebrate organization along a river was examined to relate biological responses to environmental changes observed across 2 discontinuities (a dam and a tributary). Benthic macroinvertebrates and a range of environmental variables were sampled from 4 study segments (above the dam, below the dam, below the tributary confluence, and in the tributary). Substrate was significantly coarser below than above the dam. In contrast, water-quality variables, such as water temperature and dissolved O₂, changed little below the dam. The most striking discontinuity was substrate coarseness at the tributary confluence. Substrate below the confluence was finer than substrate below the dam and similar to the substrate above the dam. Macroinvertebrate organization differed across the 2 discontinuities. Assemblage composition above the dam was more similar to composition below the confluence than to composition below the dam. The longitudinal organization of the macroinvertebrates could be explained largely by changes in substrate characteristics and habitat preferences of the indicator species. The densities of drifting zooplankton and phytoplankton were higher below than above the dam and were higher below the dam than below the confluence. However, the density of drifting plankton did not differ between the reach immediately above the confluence and the reaches below the confluence. This result suggests that the decrease of zooplankton and phytoplankton occurred above the tributary, probably because of biological entrapment or passive deposition rather than the contribution of the tributary inflow. The dam and tributary caused contrasting discontinuities in macroinvertebrate organization. The tributary generally reversed the dam-related changes to the main stem habitat and the macroinvertebrate community. A key management implication of our study is that efforts to restore dam-related environmental impacts would be facilitated by understanding the role of tributaries downstream of the dam.