I don't have any ways to adapt Water Pokemon characters to a landbased setting, but I just had the following ideas: Planet Earth is 70% water, if the Pokemon world follows suit, that's a LOT of ocean for water-based Pokemon to explore! They could go treasure hunting in sunken ruins or the deepest ocean trenches, or perhaps a world where Kyogre won the battle against Groudon and Water Pokemon can explore all sorts of sunken cities and see what land life was like in a tragic way...

As for getting them on ground, perhaps incorporate canals, aqueducts, and fountains into city designs, or create something like a wheelchair but a fishtank instead for transporting them from one body of water to another?