1 2The importance of channel non-uniformity to natural hydrogeomorphic and ecological processes 3 in gravel-bed rivers is becoming increasingly known, but its use in channel rehabilitation lags 4 behind. Many projects still use methods that assume steady, uniform flow and simple channel 5 geometries. One aspect of channel non-uniformity that has not been considered much is its role 6 in controlling backwater conditions and thus potentially influencing patterns of physical habitat 7 and channel stability in sequences of riffles and pools. In this study, 2D hydrodynamic models of 8 two non-uniform pool-riffle-pool configurations were used to systematically explore the effects 9 of four different downstream water surface elevations at three different discharges (24 total 10 simulations) on riffle-pool ecohydraulics. Downstream water surface elevations tested included 11 backwater, uniform, accelerating, and critical conditions, which are naturally set by downstream 12 riffle-crest morphology but may also be re-engineered artificially. Discharges included a fish-13 spawning low flow, summer fish-attraction flow, and a peak snowmelt pulse. It was found that 14 the occurrence of a significant area of high-quality fish spawning habitat at low flow depends on 15 riffles being imposed upon by backwater conditions, which also delay the onset of full bed 16 mobility on riffles during floods. The assumption of steady, uniform flow was found to be 17 inappropriate for gravel-bed rivers, since their non-uniformity controls spatial patterns of habitat 18 and sediment transport. Also, model results indicated that a ''reverse domino'' mechanism can 19 explain catastrophic failure and reorganization of a sequence of riffles based on the water surface 20 elevation response to scour on downstream riffles, which then increases scour on upstream 21 riffles. 22 23 JHYD Accepted Manuscript Pasternack et al., p. 3