The precautionary principle means that if there's something that is likely to cause a problem—I'm paraphrasing this, essentially—or that you can't be sure it's not going to cause a problem, you do the thing that's less likely to cause an irreversible harm. Precautionary would generally mean that you wouldn't assume that a fish or other aquatic organism is irrelevant to the ecosystem. That would be a highly risky assumption to make.
The precautionary approach would say that you assume that things matter that are in the environment and you manage around that. This is why managing for fish habitat is a very nice and precautionary thing to do, because if you're saying we can't degrade, we want no net loss of fish habitat, what you're really saying is we actually don't need to know whether this fish eats that fish or whether this thing eats that thing, because we're going to put that aside so that the fish that we're interested.... Ultimately, this serves us, because the thing we want to fish is supported by that ecosystem. The precautionary decision is something that most likely keeps the integrity of that ecosystem intact, despite our activities.