This is found in the hedges just west of the Dark Palace proper. Wait until you've complete the dungeon to grab it, as the guards will clear out.
There's another baby among the hedges - way back at the beginning, near where the first guard was. Again, it's best to wait until completing the dungeon before grabbing this.
Exit the Dark Palace region to the overworld. Use a Pegasus Boots charge into the leftmost tree to shake loose a baby.
Move west and look for this tree (there will be a Cyclops nearby). Hit the tree with a Pegasus Boots charge to knock loose another baby.
Head north to the field of rock piles; there's a baby atop one. Use another Pegasus Boots charge to knock it loose.
Continue north to the river. Hop in to find a baby in deep water by a waterfall.
Use the rift by Baby #28 to get here. Climb the ladder to the higher ledge, then merge and move to the left. When you reach the large ledge with lots of grass, pop off the wall and slice it up. There's a baby to be found here.
Merge left again the northeast ledge. Continue north to find a giant waterfall, analogous to Zora's Domain in Hyrule. Hop into the water and look in the southwest corner for another baby.
Follow the river to where it runs into a massive pit. There's a baby in stream just before the edge of the world.
Now return to Dark Palace and take the southeast exit. Turn left and merge into the cliff face above the rift. Move left until you reach the high ledge at the southern edge of this area; there's a baby up there.
Immediately east of Turtle Rock proper is a circle of Rupees. Dive into the middle to grab the baby there.
Head to the central west section of the region, straight south from the shop. There's a baby on the cliff wall here.
Jump back into the water and swim a bit further south. On the edge of the region is a purple ledge with a boulder. Lift the boulder to free a trapped baby.
Swim due east to the winding channels, and climb out of the water. Follow the purple ground south to find another baby attached to a wall.
Head to the northeast corner of the area, where the Racing Bro would be in Hyrule. Merge with the cliff face above the rift and move left. When you reach a lone skull, smash it to reveal the area's final baby.
This is immediately north of the Misery Mire weathervane. Hop over the cliff to grab it.
Swim to the southwest corner of the area. The game's penultimate baby is in the deep water here.
Exit the swampy area to the east, and you'll quickly spot two boulders. The game's final baby is underneath the lower one.