If you are going to involve both saltwater and freshies, you might do well to develop the brackish regions where both may be encountered simultaneously. Of course there are exceptions; the salmon swimming upstream, the bull shark that is encountered hundreds of miles upriver, and so on.

When one has saltwater aquariums, it used to be common to subject new acquisitions to a "freshwater dip" - placing the fish in freshwater would kill smaller parasites beneath the scales. Granted, too much time in freshwater will kill a saltie. The reverse is also true.

Maintaining proper salinity can also be a problem. Creatures trapped in tide pools, for example, must tolerate extremes in temperature and salinity as the sun evaporates the water in the pool.