Head to the ledge with the Racing Bro, then merge into the cliff wall. Move right to reach a ledge with a large boulder. Lift it to discover a baby beneath.
Hop into the water and swim towards the lake. As you round the curves of the stream, you'll spot this underwater near a ladder.
This is in the water immediately south of the House of Gales.
There's a lone tile in the northeast corner by the House of Gales. Use the Tornado Rod to flip it, revealing a baby.
This is on the cliff wall immediately outside of where you met Mother MaiaMia.
In the southeast area is a pair of columns. Place a Bomb between them to reveal a cave opening. Head inside and bear straight to find a small body of water; the baby is in that water.
One of the columns just north has a baby atop it. Knock it loose with a Pegasus Boots charge.
This is in a small body of deep water next to Hyrule's equivalent of the Swamp Palace.
Desert of Mystery
Drop south from the Desert Palace weathervane. Use the Sand Rod here to dig up a baby.
Head to the northern section of the desert. Use the Sand Rod here to unearth another baby.
Hyrule's last baby is under a rock in the secluded part of the desert, the winding "swampy" part accessible from the east. Lift the boulders here to find it.