Well, IMO water bonuses, let it be regeneration or even movement in deep water, aren't a good idea as long as your goal is to create a naga race that also is good in blizzard meele maps. The reason for this is that there are maps where there is no "valuable" water for the naga race and thus this bonus turns out more or less useless, so the Naga are in a disadvantage, while there are also maps with a lot of water where Naga might be OP. And a race should be balanced in every map. So aslong you're not creating a Naga campaign with fitting maps I would not use water bonuses.
Some ideas from me, as I see that you use this "Naga Portal" building, maybe try to make it work like the Zerg's Nydus Worm? You could even make them teleport buildings like the eldar can in WH 40k (i think so).
If you still want to have some water interaction maybe make it around rain? Not the tarrain rain in some maps, but a effect (the one from the stormcall ability?) that is around the main building, and can be spread on other buildings in range (combine this with lightnings and you have a fine defensive mechanic). Or make some stormcaller/stormsphere that somehow have this rain around them (permanently or toggeled) and give bonuses this way.
Or make every big building (not food building and towers) be guarded by a waterelemental that can't move away from the building to far and respawns after a given time if it is destroyed (defensive mechanic).
Some Unit ideas would be a gathering Turtle (a turtle with a murloc house on it, i've seen this model somwhere) that works as a mobile resource gathering point. It should be rather slow and have a restriction (like maximum one per main you building have). Maybe make them even start with three workers and one gathering turtle so they can start expanding once they clear a goldmine.
Another unit might be a heavy siege turtle (meele not ranged spitting rocks^^) which has slow but destructive attacks against buildings. Give it a charge ability that can be cast on buildings (i've also seen a turtle shell (shockwave) missile that would fit here) so you have a gapcloser for the slow moving turtle.
I hope this helps you a little. If you like this ideas just PM me, maybe some more things come to my mind ^^