Sensitivity of Off-Channel Salmon Rearing Habitats to Changing Base Flows in Low-Gradient Reaches of Central Idaho Mountain Streams

Critical rearing habitats for juvenile salmon and trout are frequently in off-channel areas of shallow, low-velocity water. Typically, these are remnants of abandoned channel positions that are still hydraulically connected to the contemporary main channel. However, the size and spatial arrangement of this habitat is strongly dependent on water stage in the main channel. In two salmon-bearing streams in the Middle Fork Salmon River, Idaho, we used a high-resolution channel DEM and a 1D fluid dynamics model to define the location, depth, total area, frequency, and timing and duration of flooding of off-channel habitat. We then predicted changes in water surface elevation in the main channel over a range of low flow discharges and remapped the functional off-channel areas at each flow stage. Measurements at nearby gages indicate that average late summer and autumn low flows in these streams have declined by about 7% per decade over the prior 60 years. Modern off-channel habitat along the 20km of study streams is not uniformly arranged, even at high flows, and the distribution becomes still more restricted in space and time as flows decline. Progeny of summer- and early fall-spawning Chinook salmon rear for up to 2 years in these streams before migrating to the ocean, with much of that time spent in the off-channel habitat. Progeny of spring-spawning steelhead use the same areas for up to 3 years. While much prior research has focused on the effects of climate change on the availability and condition of spawning sites and on water temperatures, this study documents likely changes in the amount and condition of rearing habitat. Further investigation is needed to understand the ecological consequences and whether the declining anadromous fish populations may be at some risk from diminishing rearing habitat during declining base flows caused by external forces, such as a changing climate, dams, or water extractions.