The Legend of Zelda: Twilight Princess/Hidden Grottos

Finding and accessing
Hidden Grottos are hidden holes in the ground that you can find while in wolf form with your senses engaged. When you find one, simply dig into it to enter, and climb into the shaft of light to leave.

Gerudo Desert

 * 1) This grotto is located on a raised platform south of the oasis flight landing spot. You'll find the hole in the middle of a trio of skulls.
 * 2) * Items Required: None
 * 3) * Enemies: Skulltulas
 * 4) * Rewards: 100 Rupees (Kill all the Skulltulas)
 * 5) Travel northeast (northwest in GC version) of the Gerudo Mesa warp point until you drop down into the lower gully. Look for a boulder along the wall with a trio of skulls near it. Dig in the center to enter the grotto.
 * 6) * Items Required: None
 * 7) * Enemies: Chus
 * 8) * Rewards: Free Potions
 * 9) Head down into the gully like you would for Grotto #2. In the northwest (northeast in GC version) area of the gully is a hill with a tree on it. Grapple up to the hill and you'll find another trio of skulls. The grotto is in the center.
 * 10) * Items Required: Bombs; Clawshot; Lantern
 * 11) * Enemies: Poes
 * 12) * Rewards: 2 Poe Souls, 100 Rupees (Light the 3 torches)

Hyrule Field (Eldin Province)

 * 1) Head to the north side of the bridge spanning Kakariko Gorge. Veer west (east in GC version), and in the corner, amidst a circle of flowers, is the hidden grotto.
 * 2) * Items Required: None
 * 3) * Enemies: Keese
 * 4) * Rewards: Rupees (Kill all the Keese)
 * 5) This one is tricky to find. The easiest way is to start in Kakariko Gorge and travel north to the next part of Hyrule Field (you will need to blow up some boulders if you haven't cleared the path). Then head northwest (northeast in GC version) about half way across the field. Next to some white sand is a brown patch of dirt. Dig here for the grotto. It helps to have your senses engaged while finding this one, as you can see the telltale shiny black patch.
 * 6) * Items Required: Lantern
 * 7) * Enemies: Chus, Magtails
 * 8) * Rewards: Free Potions, 50 Rupees (Light the 2 torches)
 * 9) Head north from Kakariko Village to the Bridge of Eldin. Just before you reach the arch of the bridge, turn east (west in GC version). A little bit past the bricks on the ground is another patch of brown dirt. Dig here to find the grotto.
 * 10) * Items Required: None
 * 11) * Enemies: Bombfish, Skullfish
 * 12) * Rewards: 50 Rupees, Bee Larva (Shoot down the beehive)
 * 13) Head north past the Bridge of Eldin into the valley. You'll come to a wooden bridge. On the north side is a Spinner Track. Ride it to the end, and dig in the center of the circle of grass to find the grotto.
 * 14) * Items Required: Spinner
 * 15) * Enemies: Stalfos
 * 16) * Rewards: Piece of Heart #32, Bombs

Hyrule Field (Faron Province)

 * 1) Enter Hyrule Field from Faron Woods. Head west (east in GC version) until you come to the southwest (southeast in GC version) corner of the field. There will be a small indent in the rock face with a couple grass patches. Dig between them to find the grotto.
 * 2) * Items Required: None
 * 3) * Enemies: Chus, Deku Babas, Keese, Rats
 * 4) * Rewards: Free Potions, Rupees
 * 5) In the same area of Hyrule Field as Grotto #1, head to the northeast (northwest in GC version) corner to find a circle of grass. Dig in the center to find the grotto.
 * 6) * Items Required: None
 * 7) * Enemies: None
 * 8) * Rewards: Bobber Fishing (Greengill, Ordon Catfish, Hylian Loach)

Hyrule Field (Lanayru Province)

 * 1) Take the southern exit from Castle Town. Down the steps to the west (east in GC version) is a pillar with crows flying above. Climb the vines and dig in the middle of the circle of rocks to find the grotto.
 * 2) * Items Required: None
 * 3) * Enemies: Tektites
 * 4) * Rewards: 100 Rupees (Kill the Tektites), Bobber Fishing (Greengill, Hylian Pike)
 * 5) Take the eastern (western in GC version) exit from Castle Town. On the east (west in GC version) side of this small field is a ledge. Grapple to the vines and climb up. There is a circle of rocks up here. Dig in the center for the grotto.
 * 6) * Items Required: Clawshot
 * 7) * Enemies: Helmasaurs
 * 8) * Rewards: 100 Rupees (Kill the Helmasaurs)
 * 9) Take the east (west in GC version) exit from Castle Town and head north to the next area of Hyrule Field. As soon as you enter the area, stray north off the path. You should come upon three trees forming a triangle. In the middle of these is a circle of grass patches, with a grotto in the center.
 * 10) * Items Required: None
 * 11) * Enemies: Deku Babas, Poes
 * 12) * Rewards: 2 Poe Souls
 * 13) In the same area of Hyrule Field as Grotto #3, head to the north point of the stream that flows into Castle Town. Near the cave that the water runs out of, on the east side (west side in GC version) of the stream, is a circle of grass with a grotto.
 * 14) * Items Required: Lantern
 * 15) * Enemies: Skulltulas
 * 16) * Rewards: Rupees (Kill the Skulltulas), 50 Rupees (Light the 3 torches)
 * 17) In the same area of Hyrule Field as Grottos #3 & #4, head west (east in GC version) across the bridge. Veer south, and you'll come to another circle of grass patches. Dig in the center to find the grotto.
 * 18) * Items Required: None
 * 19) * Enemies: Chus
 * 20) * Rewards: Free Potions
 * 21) South of the Great Bridge of Hylia and past the Chus are some ledges with boulders on them. Blow up the boulders and grapple your way to the end. Up here, among the a circle of grass, is the grotto.
 * 22) * Items Required: Bomb Arrows; Clawshot
 * 23) * Enemies: Bubbles, Fire Bubbles, Ice Bubbles
 * 24) * Rewards: 100 Rupees (Kill all the enemies)

Lake Hylia

 * 1) Use the cannon to launch yourself up to the Flight-by-Fowl minigame. Pay 20 Rupees to play the game and grab a Cucco. When you jump off the ledge, turn around and head under the house. Eventually you'll see a ledge you can land on. Look around on the ledge for the grotto.
 * 2) * Items Required: Iron Boots
 * 3) * Enemies: Shell Blades
 * 4) * Rewards: 100 Rupees (Kill the Shell Blades)
 * 5) On the land portion in the south of Lake Hylia, there's a ladder you can climb up to get to the Howling Stone. On the same level of land as the Howling Stone are some patches of grass. Dig between them to find the grotto.
 * 6) * Items Required: None
 * 7) * Enemies: Water Toadpolis
 * 8) * Rewards: 100 Rupees (Kill the Water Toadpolis), Bee Larva (Destroy the beehive), Bobber fishing (Greengill, Hylian Loach)

Ordon Ranch

 * 1) Head to Ordon Ranch, and in the back of the goat pen you'll find the hidden grotto.
 * 2) * Items Required: Lantern
 * 3) * Enemies: Rats, Chus
 * 4) * Rewards: Free Potions, 50 Rupees (Light the 3 torches)

Sacred Grove

 * 1) In the area you last fight the Skull Kid in (the area before the Master Sword puzzle), there is a boulder you can blow up. Below it is a grotto. This one is odd as the hole is not big like the others.
 * 2) * Items Required: Bombs
 * 3) * Enemies: Deku Babas
 * 4) * Rewards: Piece of Heart #42

Snowpeak

 * 1) Make your way to the Howling Stone and look down to the west (east in GC version). You should see a lone tree. Make your way to it, and look around the tree for the grotto.
 * 2) * Items Required: Ball and Chain
 * 3) * Enemies: Freezards, Ice Keese, Mini Freezards
 * 4) * Rewards: 100 Rupees (Hidden underneath one of the Freezards)
 * 5) Just north below the Howling Stone is a pair of trees. The grotto is near one of them.
 * 6) * Items Required: Bombs
 * 7) * Enemies: Chus, Ice Keese
 * 8) * Rewards: Free Potions