Generally by who?
Crater Lake is a pretty special lake: It was formed purely from rainwater into a crater over the last 7000 years. It is still the clearest lake in the world.
With fish, however, came a whole ecosystem. When fish die they decompose. I don't know the details, but the whole process is leading the lake to be less and less clear.
(Some people also consider it the bluest lake in the world, but that title tends to be disputed).
Just checked again and it seems you need to release any bull trout caught there, as they are now endangered. Pity.