There are eight dungeons scattered around Hyrule, each with a boss that will need to be defeated. The locations and descriptions are as follows:
Sacred Grove Temple - located in the Sacred Grove on the western edge of the Faron Woods. This forested temple will take the hero both inside a root overgrown dungeon and outside into the forest itself, leading to an ancient Bow weapon and culminating in a battle against the giant Tektite-like monster Gohma.
Abandoned Pyramid - located on the northern edge of the Gerudo Desert. This pyramid is thought to have once served a very different purpose, with mine carts and crates still scattered about. Spiral your way into the center of the structure to claim a powerful Bracelet and face the angry monster Manhandla.
Mountaintop Mausoleum - located just east of Goron City in Death Mountain. This underground area once served as the Goron's mine, but has been transformed into an area to house their dead from a horrible illness that's spreading. Make into the depths of the mausoleum, facing undead Goron foes, happening upon some powerful Boots, and destroying the evil Sorcerer who controls Vires.
Lakebed Lair - located at the bottom of Lake Hylia. Once a shrine for the Zora people, it has been taken over by jellyfish monsters known as Plasmarine. Navigate through the twisting corridors, water puzzles, and quicksand traps in order to claim the legendary Hookshot and reach the boss.
Snowpeak Caverns - located in the depths of the Snowpeak region. This cave system is accessible from an entrance in the cave face, but be careful with the frozen floors and walls (and the item that creates ice!) and be wary of the ghostly hands that drop from the ceiling. Make your way to the completely frozen depths in order to face the Stalfos Knight that has claimed this place, but don't forget to explore fully for treasure!
Tower of the Winds - located in Septen Heights. This newly constructed spiritual tower was taken over by a giant bird known as the Helamroc King. Climb the many floors, facing elemental dangers (hopefully armed with a very special Shield), in order to reach its roost at the top.
Eastern Ruins and Hyrulean Sewers - located in the area between Lost Woods and Hyrule Castle Town, and also throughout Hyrule. This complicated dungeon spans the Hyrulean Sewers in multiple locations underground as well as the ruins underneath. Find access points to the sewer near the forest, near some ruins, near a lake, and on the tip of a mountain, in order to find all the keys and unlock the rooms of the ruins. Collect your Boomerang and face the Dark Tribe wizard known as Carock.
Interloper Sanctum - located deep in the Lost Woods. Little is known about this structure that is shrouded in evil magic...
Is there a way to re-enter Lakebed Lair after beating the boss?
Edit: After getting flippers you can swim back in.