We have floors similar to previous posters - hard clay, sand, rubber mats, sawdust. None of our stalls are sized to fit the mats perfectly - we had to
cut mats in all of the stalls. Try to avoid having small pieces of mats to fit gaps. The small pieces get moved easily. We don't have a drainage problem, exactly, but we do get wet sawdust underneath the mats. Every month or so we end up picking up the mats and cleaning under them and repositioning them. This will all be avoided if the stall dimensions were something like 12x12, so mats fit tight without cutting. Cutting these mats is usually cumbersome & awkward. I use a long metal ruler and bend the mat over a board to help open up the
cut as I go. As mentioned in other posts on
TBN, its better to make many repeated shallow cuts than to try to make a single deep
cut.
Some horse people, and a study quoted here on
TBN, say it is ok for the horses feet & legs to have the rubber mats over concrete. And with concrete you are assured of a correct pitch for your drainage, and the rubber mats won't shift or slide as much as they would on gravel or sand. There are a series of horse barn books from Cherry Hill that recommend making 'tacks' by welding metal washers on top of nails and then using these to pound down into corners where rubber mats meet (obviously only needed if you don't have concrete under the mats). Based on recommendations from horse people I know and these books, I think that rubber mats are a good thing, both for the horses leg & foot health, and also to help make cleaning stalls easier (easier to use a pitch fork to pick the stalls clean). We go the extra mile and use our own routine for stall cleaning that gets it as clean as possible while preserving as much good sawdust as possible. We use the pitchfork (actually a horse manure fork from TSC) to pick off the easy to get, large pieces of manure, then use a shovel to first carefully scrape away only the top inch or so of sawdust until we find a urine-soaked spot, then use the shovel to completely remove all of this wet sawdust down to the rubber. Then we sift some PDZ stall cleaner/refresher onto the wet spot, and then clean the rest of the stall. I can see I'm writing a book here. Anyway, we are particular. I'm certain that we prevent leg & foot problems by keeping the stalls dry and 'cushiony'. Again, if you have not yet built the stalls, I highly recommend making the interior dimensions a multiple of the 3x4 mat size - a 12x12 stall will work great.
We previously used the wood pellet bedding and loved it - it is the easiest to clean, but we stiched to sawdust when the price of pellets went up when people switched to wood stoves.
Pete
Re: Floor Options for Horse Stalls? 
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