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