On the San Clemente Creek side of the reservoir, the half-mile reach between the dam and the downstream end of the Reroute Channel was reconstructed to carry the combined flows of both the river and the creek, and to allow for fish passage. First, the sediments were excavated down to the pre-dam elevations. In order to facilitate fish passage, a series of step pools were created along this reach. The step pools were created by placing large boulders across the bottom of the channel. In high flows, water flows over the boulders creating small jumps for the steelhead. Behind the boulders, water pools, creating an area of slower moving water where the fish can rest before taking the next jump. This design is based on naturally-forming step pools that can be found further upstream in steeper reaches of the Carmel River.
Along both the reconstructed reach of San Clemente Creek and the bypass channel, measures were taken to restore and/or establish riparian habitat. This included creation of seasonal ponds that can be used by California red-legged frogs. The ultimate goal was to create a dynamically resilient riparian corridor. In other words, the design assumes that while step pools, frog ponds, riparian habitat and other features may be changed by high flows, the system will naturally re-establish itself in such a way so that the functions of fish passage, sediment transport, and habitat support will continue to be provided.