Depending on how far into the game you already are, there are ways to make it easier to dig through or drain water to make way for whatever you want to do.
With enough luck and courage this can be obtained right from the start of the game by running to the ocean and doing a suicide/log out dive and one of the chests might just have it. Optionally large pools of water around might also have water chests that contains this if you search around.
With Flippers you can dig downwards till you are almost out of breath and just swim to the surface and catch a breath. Repeat that process a few times and eventually you'll dig into a large enough cavern to drain those water away.
Flippers can also combined with Diving Helmet later to make Diving Gear which also increases the duration you can stay under water making it even easier.
This is also obtainable very early into the game, if you are lucky, some random chests or pots around might just supply you with some. If not so, you can combine Coral obtainable by diving slightly into the ocean with Waterleaf which can be found in the dessert together with Bottled Water which can be found around or by filling Empty Bottles near pools of water.
Application of Gills potion is even easier, once used just spend the next 2 minutes digging down and draining the water away from where you do not want it.
If you are already well into Hard Mode, crafting a Neptune's shell effectively combines both the previous items I suggested together and allows you to freely move indefinitely in water.
If slowly digging your way through is not what you have in mind, I can also suggest
Sometimes you might find it hard to drop the dynamite exactly where you want it. You can combine it into an Explosives. But needless to say this will result in almost every tile in the area being removed - except for tiles immune to explosives. You'll have to build back the entire area from scratch after using dynamite.