The theory that rotten water caused disease was very popular in the Middle Ages. The theory took a bit of hit in 1897 when Ronald Ross showed Malaria was transmitted by mosquitos not swamp gas. But it made a bit of a come back in 1918 when swamp gas was blamed for a flu outbreak by some public officals who had training in making stuff up to scare people and make themselves look smart.
Rotten water can be dangerous of course. If say the rotten water is from a break in a sewer line. Don't crap in your pond and you'll probably be OK.
Rotten water from the break down of plant material in a pond is basically the same as a garden compost pile. You know, that organic stuff. A compost pile can contain diseases, bacteria and virus of course. So can garden soil, the kitchen table and sand boxes. But if you keep certain things like human waste and meat out of your compost pile it won't kill you.
Only some bacteria harmful to humans. Bacteria in a pond generally do not attack humans. Muck in a pond does smell and looks the same as sewage, but very different
when it comes to transmitting disease. Mosquitoes are a much greater threat.