What level of Fish Environment do you have right now? When you click on Research Environment, do you see "You have Level two" or do you see "You are researching Level two" displayed on the left? The improved Fish Environment doesn't take effect until research is complete.

The only other thing I can think of is that you're either overfeeding or underfeeding your fish. When you put a fish in the isolation tank (or click and hold on it in the main tank), you'll see the two meters displayed for that fish: Health and Fed. If you feed a fish before it gets hungry (the bar turns yellow), the fish will lose some of its health. You can kill fish that way, or hasten the death of a fish that is losing health for other reasons (such as sickness or inadequate Fish Environment for that species). If you don't feed your fish often enough, starvation will cause them to lose health.