Is yours a walk-in run, or a run attached to a coop, Fuzzyfelt? If the base is very wet, so are the birds, and its very unpleasant for them and for you.The smaller the run, the more of the base will get wet when the rain blows in sideways through uncovered areas, or runs off a roof with no gutter and then blows in. The only answer, especially in a small attached run in winter, is to increase the area of the sides covered by clear plastic tarpaulin. This is effective at giving shelter from wind as well as rain, and so long as one side is left open for air, (one of the shorter ones, perhaps,) the base will dry out better. The clear tarp lets nearly all the light in and is easy to fix. Try Tarpaulins Direct for strong, clear Monotex tarps in many sizes. http://www.tarpaulinsdirect.co.uk/monotex-tarpaulin