Sediment transport is highly variable in space and time and a natural part of the river environment. Important linkages exist between sediment transport processes and riverine aquatic habitats. If the sediment load or bed sediment type changes, there are usually ecological consequences. The responses are usually complex, long lasting, and may be beneficial or detrimental to a given resource. Undesirable consequences of water projects that modify sediment size distribution or load may be avoided or mitigated when designers know about the relationships between aquatic habitats and sediment transport. Accordingly, this paper has summarized knowledge linking sediment transport and aquatic ecology. Often hydraulic engineers and aquatic ecologists have dissimilar frames of reference for the evaluation of river systems. However, this brief report should provide a common footing for hydraulic engineers and the environmental community in the evaluation of streams and aquatic habitats.