Weevil

Best answer as chosen by Asker / Ratings
It's impossible to miss out on any of the Small Keys. I can only remember a few locations of the Small Keys.

The first one should be in the room where you meet Princess Ruto. Once you drain the water level to the bottom, use Din's Fire to light the torches. Enter and defeat the enemies.
The second one is in the same room. The water level has to be at the middle level, so that you can bomb the crack in the wall.
Another one that is often missed is inside the tower in the centre of the main room. After raising the water level inside the tower, use the Iron Boots to sink through the hole where the floating platform was. Defeat the enemies that drop from the grates to get another Small Key.
In the room with the rotating water, jump in the water with the Iron Boots. Stand at the base of the metal slope, take off the Iron Boots, rise up the slope, then put the boots back on. Angle yourself so that you can hit the switch in the dragon's mouth and grab the metal ring with your Hookshot. Get past the enemies behind the grate and rise up to find another Small Key.