He's a Quarter horse, 15.3 hands, not naturally big or really lean. He doesn't have a lot of hindquarter muscle. He was off work for almost 2 months until last month and he lost a lot of weight and muscle from that, and I don't think he's gained it back yet. I'm training him for hunter under saddle, a bit if western pleasure.
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What do you do with him now, exercise wise? Do you have access to any hills, deep sand, any kinds of trails? Although arena work can build muscle, I've always preferred to go out onto the trail where all the rougher terrain is. It makes your horse have to carry himself a bit better, if that makes sense... It's the difference between going for a jog on pavement and going for a jog cross-country, both are work and both are necessary, but while on the pavement you can work on your running style/ form and not have to worry too much about where you're going, not only do you work more muscles going cross-country and you have to have a bit more control over your body/where you put your feet/how long your strides are/etc.
If you can, I would maybe take one day for working in the arena, going over trot poles, maybe do some small jumps, basically schooling, and the other two for going out trail riding. Going up hills is especially good for their back ends, as is trotting through deep sand. Try to keep the pace on the trail at a steady trot, although in the beginning you'll probably have to take it easy with him.
One exercise I like to do with my horse is working in a spiral- just going in a circle, and every x time around, making it smaller, until you get to a point where he's turning on his haunches right in the middle. You can either work your way back out or stop at that point. Just start at the walk, then work up to doing it in the trot, then the canter. I like this because it not only helps my horse to move off of his front end (he's built downhill), but it helps us to be as exact, as I try to make the circles just inside his last circle (his second hoof prints should be just inside his last circle of hoof prints, maybe a couple of inches between them) and so it always helps both of us use more precision.
Transitions are also very good. You can start with easier ones, like walk/trot/walk, and eventually throw in halting, the canter, etc.- I personally really like going from a halt to a canter to a halt. You can also try cavaletti, and even though you're doing HUS and WP, going over some low jumps won't hurt. They don't have to be high, just big enough that he has to lift up and push himself over with his back end.
As for how long until you see results, I generally give the horse at least the same amount of time they had off before I even bother really looking for results- so, since he's been off for pretty much two months, I wouldn't expect anything at all until at least 2 months have gone by.