Did not houseruling Electricity gets a save bonus (same everyone getting a penalty to save) water make the battle harder?
There is a good chance that it wouldn't have been that bad if you didn't change it.
Plus, you are talking about a flooded room with water elementals. Giving them bonuses makes them tougher.
No, I gave a situational saving throw penalty against electricity effects for being entirely in water, which caused in at least one instance a failed reflex save on the part of the elementals when it would have been a success. Of course, this could have been bad for the PCs, too, so the Bard had to carefully aim the spells (and coincidentally had trouble hitting both elementals without also catching party members, leading him to use the "electric balls" on only one). Since the water elementals had no electricity powers of their own, I fail to see how that did anything to make them more powerful.
If the entire battle field is filled with water, that really favors water elemental and thus EL should be adjusted accordingly. I say it worth EL +2 at least. So resulted EL will be party level +4 and that means the party has 50/50 chance to win. So, TPK could be possible.
I figure you encounter creatures in their preferred settings, so the CR should represent facing a water elemental that's in the water. Out of water, they're pretty pathetic, save for sheer hp and DR. And I left land spaces. Described in detail below, if you care.
[sblock]The battle scenario was partly inspired by Zelda: Windwaker, when the tower's flooding up and you're running up along the spiral staircase as the giant bird monster harasses you. I left a 5 ft wide ledge along the perimeter of the tower wall just above the water level so there would be standing room, as well as being able to access the escape ladder from there. Furthermore, if a PC had gotten pulled to the bottom by one of the elementals, the entranceway they originally came into the tower from was too small for the elementals to follow through easily, and I made sure to have a higher point shortly before said entrance that a PC throw to the bottom could swim to to get out of the water to safety. The PCs should have been aware of it, as I made them make climb checks to get down it before entering the room. I was keenly aware of the dangers of a PC getting swept up and trapped by whirlpools or drowning, and made sure to put in safety features. For its part, the room was part of the villain's set up, and this particular villain (inspired by yet another game, Booster from Super Mario RPG) was almost childlike and just wanted to "play" with the party as they climbed up his tower. So, after fighting and losing badly, the party figured out to get out of there (and struggled to rescue the two PCs still trapped in the water), if they had to actually fight it, even with the dry points to stand on, it'd have been an amazing TPK.[/sblock]