I worked in a barn that had a trench like a dairy. They put a grate over it and it was great. We would wash down the barn and squeegee the water into the trench, which was better for the concrete. We were also able to sanitize the barn which we had to do a few times a year for no reason and once for a sick horse. I would try to put a grate on it personally. Remember also that cleaning a barn is a full time job. If you can keep your horses outside and have the barn set up for tack, some feed, cold nights, and getting ready for shows it's a lot less work for one person.