I would agree with Paul, the floods have an impact on the river bed (snags, holding areas etc), which then has a knock on effect to where the fish want to be.
On one stretch I fish, there was a huge snag about 10 yards long that came 3-4 feet off the bottom of the river. After the 2007 floods, all that was left was a depression in the riverbed left by whatever was there. This is one example that could be identified, and I wonder what other effects there are that we can't.
On a different stretch, there is a section of river about 200 yards long that holds a decent head of fish. From the beginning of July last year right through to the end of the season it seemed barren (for barbel), but then in the last week a few turned up again. Were they always there and not being caught, or had they vacated for a while?
This for me is the challenge of the Lower, and what keeps me coming back for more!