It sounds like you're hiking in an area where there's a lot of agriculture?

I go into the Sierras, where cattle frequently graze in the foothill areas but tend to spread out over a large area, or in national parks, where there is no ag or manufacturing. I have trusted my water filter so far as the water is coming down out of mountains and the only (minimal, some say) danger is from contaminants like bacteria or protozoa, which filters do remove. Some areas have mines or logging, but it's easy to be informed about this and steer clear. Ultimately there is no ironclad guarantee, but I feel pretty safe about filtering the water. No one's spraying the mountains with pesticide.

There is someone in my group who feels the same as you who dayhikes with us and gets very sore shoulders carrying a lot of water in a daypack. If we were hiking in the valley, where there's ag as far as the eye can see, I'd be doing the same - but we're not. Sources make a huge difference.

Maybe there are places you can hike where the water sources are less impacted?