Water physics tend to differ quite a bit between the games. I did a bit of testing on some of the games here:
In Mega Man 1, it causes a lag frame every fourth frame, so effectively the game speed is cut by 25%. The physics otherwise are unchanged as far as I know (except in some zipping situations)
In Mega Man 2, it causes a lag frame every fifth frame (20% reduced game speed) and gravity is cut by 0.46875 (from 0x40 subpx/frame to 0x1E subpx/frame). In other words, gravity is cut from 0.25 (64/256) pixels/frame to 0.1171875 (30/256). Additionally, jump initial velocity is increased from 04.DF (4.87109375 px/frame) to 05.80 (5.5 px/frame).
(See also
Wiki: GameResources/NES/Rockman/Data).
In Mega Man 3 and on, water no longer causes an overall slowdown. The velocity and gravity numbers are probably different, but I don't know about the numbers in these games offhand.