I'm not a plumber, but my mom has a similar drain in her basement. It goes out to the main sewer line. If tree roots get in the pipes and clog them up, the water from toilets (yeah...), showers, and the washing machine can't get out and backs up into the basement.
More than likely, due to all the flooding, the sewer system is backed up and the water is coming back through that drain into your basement.
I would consult a plumber, though, before you think about filling it in.