If you have items that can turn poisonous water clean and vice versa, there's a lot you can do with that. The most obvious would be purifying poison so you can swim through it, but making other things interact with it would be more interesting.
There could be plants living off the water. Poison the water, and the plants wither and die. Then they can be burned to clear a path. Purify the water, and they're revived. Then they might grow vines to create new paths, or they could be used as hookshot targets.
There might be monsters living in the water than can only be defeated by poisoning it. Similarly, the water itself might spawn monsters (like
Kyamerons) depending on the state of the water.
Differences in density could lead to buoyancy-related puzzles. Perhaps some blocks float in poison and sink in clean water. They might also behave differently when frozen or evaporated.
And speaking of vapor, there's ventilation. Can Link even safely enter a poison-filled room without a fan running? And if there are fans, where does the poisonous air go?