Impact of flow regulation on stream morphology and habitat quality distribution

The importance of interactions among stream hydrology, morphology, and biology is well recognized in studies of stream ecosystems. However, when quantifying the impacts of altered flow on aquatic habitat, results are often based either on combined changes in topography and flow, or with altered flow over static topography. Here, we study the potential beneficial effects of restoring unregulated flows on salmonid habitat and separate the relative influences of changes in flow vs. topography. We hypothesize that flow restoration will increase topographic complexity and that the coevolution of topography with altered streamflow will produce stronger changes in habitat than predicted for static topography. We address this hypothesis by quantifying spawning and juvenile rearing habitat distributions for Chinook salmon (Oncorhynchus tshawytscha) from a set of quasi-three-dimensional hydromorphodynamic models for two morphologically distinct reaches along the Lemhi River, Idaho (USA): an engineered, straightened, plane-bed reach, and a less-altered, meandering, pool-riffle reach. Sediment transport was modeled with hydrographs predicted for actual interannual variability of flow and for a synthetic annual flow representing the ensemble actual hydrographs for 60 years of regulated and unregulated flows. The actual and synthetic hydrographs predicted from the model produced similar morphologic results, which implies that interannual flow variation and hydrograph order did not have a strong effect on the modeled topography. Unregulated hydrographs enhanced the geometry and frequency of pools in the meandering reach compared to regulated flows. These morphological changes did not increase habitat quality predicted from suitability indices, but the large growth of pools likely improved winter refugia for juvenile salmon. In the straight reach, both regulated and unregulated scenarios resulted in a plane-bed morphology, suggesting that flow restoration in highly altered reaches is not sufficient to improve ecological function.