Flood control projects often rely upon concrete channelization to increase the rate at which floodwaters pass through lotic systems. However, channelization results in 1) loss of reach-level structural complexity, 2) simplified flow patterns, and 3) decreased availability of microhabitats. All three of these factors have the potential to negatively affect lotic organisms. The use of interlocking concrete cell mattress provides substrates that are as stable as concrete slab, but which contain substantially more complex microhabitats suitable for aquatic organism colonization. To determine the impact of substrate type on lotic communities we evaluated macroinvertebrate assemblages from three comparable waterways in the Santa Clara Valley, CA: the Guadalupe River, Los Gatos Creek, and Permanente Creek. Non-metric multidimensional scaling of the benthic macroinvertebrate assemblages collected from four different substrate-types indicated a gradient of taxonomic diversity and community structure. Macroinvertebrate diversity, species richness, and species evenness decreased, while species dominance increased with decreasing habitat diversity, with concrete slab < concrete cell mattress < disturbed natural substrate < relatively undisturbed natural substrate. The benthic assemblage supported by the concrete cell mattress more closely resembled the assemblage collected from natural substrates than the assemblage collected from concrete slab substrates. This study indicates that even in highly engineered channels using concrete cell mattress in place of concrete slabs can increase microhabitat suitability.