You can buy ten Magic Beans from the Magic Bean Salesman in the west side of Zora's River. There are ten spots of soft soil in Hyrule where you can plant a Magic Bean. This page lists all ten locations. Unless otherwise noted, you can get a Gold Skulltula from the soft soil by catching bugs in a bottle and dropping the bugs on the soft soil

1. Zora's River: Next to the Magic Bean Salesman - In the west side of Zora's River, you find the Magic Bean Salesman. There is soft soil next to him where you can plant a Magic Bean. NOTE: there is NO gold skulltula in this soft soil, so don't drop bugs there.
2. Kokiri Forest: Behind the Shop - Look behind the shop in Kokiri Forest where you bought a Deku Shield. There is soft soil there.
3. Lost Woods: Near the bridge into Kokiri Forest - If you go into the Lost Woods and turn left, you will see a skull kid standing on a stump. Go through the hollow log and you will find a soft soil spot. You can see the bridge into Kokiri Forest here.
4. Lost Woods: Near the Forest Stage - From the entrance of the Lost Woods, go right, left, right, left, and left. This will take you to the area where there are a couple of Business Scrubs. There is soft soil behind one of the Business Scrubs.
5. Kakariko Graveyard: Behind the Graves - After you enter the graveyard, go to the first row of graves, then turn left and go to the wall. Turn left to find soft soil at the end of the row of graves.
6. Dodongo's Cavern Entrance - After you use a bomb flower to bomb open the entrance to Dodongo's Cavern, you will find a spot of soft soil just inside.
7. Lake Hylia: In Front of the Lakeside Laboratory - There is a tall house near the entrance of Lake Hylia. There is soft soil near the door of that house.
8. Death Mountain Crater: Near Warp Spot - You need to learn the Bolero of Fire to reach this soft soil. To learn the song, go to Goron City as an adult and throw a bomb to stop the rolling Goron. Then go into Darunia's room and pull the statue away from the wall. Go through the tunnel behind the statue. Use the Hookshot on the wood above the far side of the broken bridge. Sheik will teach you the Bolero of Fire. Then go to the Temple of Time and put the Master Sword back into the pedestal. Catch some bugs in a bottle, make sure you have a Magic Bean, and play the Bolero of Fire to warp to the crater. The soft soil is near the warp pedestal. You can only stay in the crater for a short time because of the heat, so drop the bugs into the soil and plant the Magic Bean quickly.
9. Gerudo Valley: On the Riverbank - Go to Gerudo Valley and pick up the cucco. Float down to the riverbank below the big bridge in Gerudo Valley. You will find a ledge that has a Gerudo and a cow on it. There is also some soft soil here.
10. Outside of Spirit Temple - Just outside of the entrance to the Spirit Temple, you will find a spot of soft soil. You will need to use the Requiem of Spirit to warp to this area as a child.