What if water mana nodes could only be built on water and a few other mana nodes like perhaps life, nature, and chaos were allowed to be build on water?
Then if you just had some mana randomly appear in water tiles, and gave workboats or arcane barges (and in addition any acolites who already have water walking) the ability to improve the mana you would have a strategic water resource.
One might also bring back the oil resource and allow both it an whales to give access to a "greek fire" upgrade for siege weapons, and perhaps a some specialized "greek fire" type units. Of course, the traditional wells wouldn't fit in thematically..but a nice everburning tile might be a nice change.