The rain poured, the river flooded over, the wind blew hard against that house, and it fell.
I know what the word "flood" means. But what does "flood over" mean?
You could also say 'The river burst its banks'.
'...the river flooded over' is not idiomatic to this native speaker at least.
Where did you find it, Sitifan?
When it floods, it overflows its course. Otherwise, it's not a flood, it's just a high-water mark. Therefore, omit the "over" from the sentence entirely. The river flooded, or it flooded its banks, or it flooded the town.