My gelding used to be TERRIFIED of the spray bottle!! He's not as scared anymore now that I figured out the correct way to get him used to it. He still gets bug eyed whenever he sees me approach him with it, but he doesn't try to run away like he used to.
So. The trick is to desensitizing is to accept the fact that you may have to scare your horse to get him used to something. Don't worry about scaring him. Worry about him hurting himself in someway. Just don't overthink it!
What I did was just get my horse attached to the lead rope, hold it in between my arm and my rib (my preference), take a spray bottle filled with water (unless you want to waste all 5-10 bucks of fly spray, be my guest!), and rub them with the spray bottle. My gelding was scared of that (weird I know, but that's my boy for ya!), but he got over it at one session. Do that both sides, but don't start on the other side until your horse is used to it on the side you started on first. Once he was good with that, I'd take a small break (like 5minutes) then I'd start again with the rubbing. Most horses would just stand there and not even blink after the second try of the rubbing. So, then you start spraying. AWAY from your horse. Don't stand directly in front of them, but face their shoulder and just act like nothing important is going on. Spray behind you until your horse is used to it. Then try the other side. Do it until he's used to it. If he moves away from it like he's scared, DONT stop. Just keep your arm away from him and continue spraying. Once he stops moving, stop immediately and praise him like crazy!!! Use the praising time as your break. I praised my gelding at
least for 2-3 minutes. Once you're done praising, try again, but closer, with your arm at your side. The repeat the steps over and over until he stands for you with no problem (:
This isn't going to be a one day thing, it'll take more than one day with 10-20 minute sessions at least twice a day. My gelding took a week and a half. Most horses take less than a week. That's just how my gelding is! Haha