Here are the locations of all the normal fairy fountains and where you can get Big Fairies.
Hyrule Field-Under a boulder near some trees, use bombs.
Kakariko Graveyard-In the grave where you get Hylian Sheild, blow up wall behind it.
Zora's River-Up top where the big boulder is. Use bombs.
Sacred Forest Meadow-Near top of maze, in grotto on ground surrounded by walls. Use bombs.
Zora's Domain-Play the song of storms on island in middle.
Gerudo Fortress-Behind pair of boxes, play song of storms.
Ganon's Castle-Under Bridge and back through wall. Use Lens of Truth.
Gossip Stones-Play the Song of Storms, Zelda's Lullaby, or Epona's Song at a Gossip Stone and a big fairy will come out.