Dikes and levees reduce the amount of room that a river meanders through. Not to mention much of the Reservation is sitting right on the floodplain. Floodplains act as "reservoirs" for excess water. When you have dikes and levees the river is channelized and so heavy rains cause the river to rise rapidly and thus you have flooding.

I'm not familiar with the Skokomish watershed, but was wondering if engineered logjams could help serve as sediment traps. Perhaps the state should buy out land adjacent to the river if possible and rehabilitate the riparian zone.