If we raise the level after the seeds sprout, they are drowned. Many aquatic insects have a very short adult phase in their life cycle. They have to synchronize emergence to be successful at finding mates. Constant temperature water from deep-release reservoirs provides no cues for synchronized emergence. We have reduced lateral migration of meanders without changing the rate of succession in riparian habitats.
Early stages convert to later stages which are often converted to agriculture.
It seems there are two basic alternatives to dealing with rivers. The Nile Valley remained productive and a center of civilization for 8000 years. Riprap the bank to prevent erosion. Despite all our efforts, flood damage has increased, rather than decreased.