Water-based bottom paint can be applied over a marine epoxy primer (for example, an epoxy barrier coat primer), as long the epoxy primer is completely cured, sanded with 80-grit sandpaper, and solvent-wiped with the solvent recommended by the manufacturer of the water-based bottom paint. If the epoxy primer is not completely cured then sanded, there's a chance that the uncured epoxy in the primer may react with the water in the bottom paint, preventing one or both of the products from curing properly, or compromising the bottom paint's adhesion to the epoxy primer.