On top of the logistics of moving massive amounts of water around, flood water is typically highly contaminated - by their nature, floods sweep up everything in their path, which typically will include things like:
Soil and sand (a massive pain to filter out)
Agricultural run off (manure, pesticides, fertilizer, …)
Raw sewage (from treatment plants that tend to be near waterways, or just from damaged infrastructure)
Industrial wastes (from existing plants, or old contaminated sites)
Infectious disease is a major problem after a flood, partly because of infrastructure damage but also just because so many people will have come in contact with contaminated water - you don’t want to irrigate your crops with flood water, much less drink it