Be Methodical
The biggest annoyance in the Water Temple is the constant need to change the water level to access different areas. To minimize your need to repeat this dungeon drudgery, make sure you have visited every accessible part of the dungeon when you have the water set to each level. This includes diving down with the iron boots when the water level is high, because sometimes the water lifts parts of the dungeon floor up, revealing hidden chambers -- as in the dungeon's central room.
Watch for Weak Walls
Bombs are a useful tool in any "Legend of Zelda" game and in the Water Temple they are particularly useful. In this dungeon, there are a few walls that are bomb-able and what lays behind them should not be missed. Some of these walls will have large cracks in them, but others will only be noticeable because they are a different color from the rest of the wall around them. They also sound different when struck by your sword. Keep your eyes peeled -- and your sword drawn -- to find these bomb-able walls and then blow them away to discover the treasures that they conceal.
Keep an Eye on Your Keys
Because the Water Temple is a labyrinth made more challenging by its water-level puzzle, you may find yourself keyless and faced with a locked door. To avoid this, always be sure to check all accessible areas when you do have keys with you. Otherwise you might get to a point where you have almost completed the dungeon but need to go comb the entire place once more for a final, previously missed key.
Din's Dive
The constant need to change between your regular boots and iron boots combined with the Water Temple's water-level-changing puzzle makes this dungeon particularly bothersome. However, you can also sink to the bottom of pools of water by exploiting a glitch in the game known as Din's Dive.
Stand on the edge of the platform in the main room of the dungeon. Just as one of the Tektites in the room is about to jump into you, cast Din's Fire. The Tektite will knock you off of the platform, and during the spell's animation you will fall through the water to the dungeon's first floor. Once you have control again, quickly swim to one of the openings on the lower or middle floor of the main room. This glitch can be exploited anywhere in the temple, as long as there is an enemy to knock you off of a platform while you cast Din's Fire.