We've all seen the small balloons that kids fill with water and launch them at their pals, water bombs I think they're referred to. They are made with latex rubber, just like your standard latex rubber party balloon. There isn't an issue filling the water bomb balloons with water as it's unlikely the filled balloons will remain intact for very long. Fill with water, launch at your pal, the job of the balloon is over.
However, long term contact with water, which is what you propose, may be a different thing altogether. The latex is a naturally occurring substance found in trees. Excessive moisture and/or sunlight (uv rays), can degrade the latex over time, I couldn't put a timescale on it but it will degrade. The elasticity of the balloon will diminish and eventually it will fail. What this failure would mean to your filter I don't know as you don't give details of how you plan to use the balloon.
I'd just be cautious. The balloon might last for weeks and weeks, even months. You could use the balloon and maybe replace it every so often so the long term effect of degradation wouldn't be an issue.
But I must admit i'm curious now how you plan on incorporating a balloon into your filtration system.