After you arrive in the Minish Woods and meet Ezlo, you continue on to the first dungeon, Deepwood Shrine.
In the first room, push the bottom totem left to pass. Next, beat or avoid the slugs and press the four switches next to the unlit torches (the switches are to the left and right) to reveal a chest with a small key inside. Go up to the locked door and press R in front of it to open it with the key.
In the next room, a couple slugs will fall from above, so watch for shadows. Note that you can't swim yet, so don't fall in! (Luckily you don't lose any hearts if you fall in.) On the wall above is a lever that Ezlo tells you to grab and pull with R. Walk up to it, press R, and press down to pull it. The bridge will be revealed. Across it you find a mushroom. What to do with it? Here's what: grab it with R, press right to pull it until it doesn't go any further, then LET GO OF THE DIRECTIONAL PAD to be thrown across (don't let go of R, that doesn't get you anywhere). You'll end up on the other side of the water (another slug will fall so watch out). Exit north.
In here, go right and watch out for the mushroomy monster; the only way to kill it is to throw a pot at it. Go up the stairs to the platform here and press the switch to light the torch and burn the vines on the barrel. Now get in the barrel, and go through the other exit inside. There are more mushroomy monsters here, so avoid them too and go down to another platform with a torch, this time with two switches. You have to move the totem onto the top switch, so walk past the top switch and push the totem. Then stand on the bottom switch and the torch will be lit, burning these vines and freeing the barrel.
Get back inside the barrel and walk up to roll it a little bit up until the exit is to the bottom left. Go through and exit southwest.
Beat the red monster if you want, and take the top left path. Pull the mushroom ALL the way down so you reach the top of the room. Go up the stairs here and open the big chest for the dungeon map. Then walk down and jump off over by the mushroom. This time pull it about halfway down (you should be standing on the little break in the line on the floor) so you land on the middle strip. You'll want to take the door to the left.
In this room a couple more slugs will fall, and there's a red flying monster you'll want to get rid of. To hold down the switch, you have to push the pot to the right until it's over the switch. The bridge will be revealed and you can exit south.
This room is a bit of a puzzle because when the two switches are pressed, the chest will appear on the tile inside the box. After pushing one totem onto one switch, you have to grab the other totem with R and pull it out, then go on the inside of it and grab it and pull it in over the switch. Get the chest for a small key, then push out a totem to get back out. Go back to the barrel room (pushing the block out of the way when you have to.
Get inside the barrel and roll it until there's an exit to the upper right. Take it, then head east and use the key on the door.
In this room there's a mushroom that takes you south, as well as a path north you can take. Use the mushroom first, but be careful not to pull it too far or you'll overshoot and land in the water. Pull back to about the end of the line on the floor. From here, step on the switch to the left to reveal the bridge above, then pull this mushroom up the bridge all the way to reach the ledge below.
In the next room, slugs will fall in addition to the two already there, so kill them all. Above, pull the right hand totem PAST the switch, then go around and push the left one onto the switch and go through the door. Three red monsters will appear, so get rid of them (they may scoot around the floor a bit, so watch out) and the other door will open and a small key appears. Grab it and leave.
Now take the path up the stairs. Jump off the ledge and go through the door, killing the red beasts if you want. Go down the stairs in the north wall. To get the big chest here, push the right block up and the left block left. Inside is the compass. Push one of the pots onto the switch to reveal a chest which you can't reach just yet. Go back up the stairs and take the door in the west wall.
In here, avoid the mushroom monsters (be careful: four will appear in a square near the entrance) and step on the switch to open the door below, but don't go through it yet. Go through the locked door to the west.
When you beat it, you win the Gust Jar: a strange device that sucks in air, then blows a little gust when you let go of the button. This item can be used to clean off dusty and sandy spots on the floor (sometimes revealing switches or other things below), can suck in pots and rocks and some enemies, and can even draw in those mushrooms you pull to reach far spots.
Use it now (hold down the button for a while) to get rid of the spiderwebs, two of which block doors. First take the south door for a piece of heart, then go back and take the east door to get back in the room with the dust on the floor. You can use the gust jar to beat the mushroomy enemies, by drawing them in until they turn grey, and hitting them with your sword. Clear away all the dust to reveal some switches, which make chests appear containing Mysterious Shells. Later on these shells can be used to trade in for a chance to win figurines. Another revealed switch will create a blue warp from the entrance to this room. Before going further, go back through the door to the right and clear away the dust to reveal a switch, step on it for a chest with 20 Mysterious Shells. Back in the blue warp room, exit through the south door to return to the barrel room.
Get inside the barrel. Before using the Gust Jar on the spiderweb, roll the barrel until there's an exit to the upper left. Go through, suck up the one dust spot in the center, step on the switch and you get another 10 Mysterious Shells. Back inside the barrel, roll it until you see the exit with the spiderweb over it. Use the trusty Gust Jar to get rid of it, and drop in. To get further, suck the giant lilypad towards you with the Gust Jar. Stand on it, and to propel yourself, tap the Gust Jar button to let out a gust of air. Move the lilypad over the waterfall, watch out for the flying red monsters (Pestos) and when the path splits, go right.
Get to the stairs up, take them and get rid of some of the pots so you can push one onto the switch. Back on the lilypad, go through where the bars were. Propel the lilypad to the end of the water, where you can now reach the chest with a small key in it. Get back on the lilypad and go back out to the big room. This time exit north, watching out for falling slugs. Unlock the door and go through.
Pull the mushroom all the way down to get to the other side. You would seem to be stuck now, but as I mentioned, the Gust Jar can suck in those mushrooms, so do that with the one to the right, and repeat with the rest (make sure you're a little distance away from the last one or you'll fall into the water). Get the big chest for the big key. Step on the switch below to create a red warp. Step on it to get to the entrance, then take the BLUE warp which takes you to a previously unreachable piece of heart (which may be your fourth). Then go on back to the blue warp to get back to the entrance.
Use the Gust Jar to get rid of the webs over the two doors to the left and right. First go up the left stairs. Push the block in front of the chest to the right and get the 20 rupees inside. Then go back down the stairs and through the stairs to the right.
Use the Gust Jar yet again to draw in the mushroom, then go below the mushroom, stay a little distance away, and use the Gust Jar again to get to the boss door. When you're ready use R to unlock it.
The strategy with this boss is to carefully avoid its jumps (it's tricky; watch for it to stop moving. You can keep it from jumping too much by staying a little close) and use the Gust Jar on its base to make it smaller and smaller until it starts to wobble and eventually falls over (it will try to land on you so be careful not to stay too close at this point). When it falls, hit it with your sword a bunch of times and it'll get back up. Repeat the process until it's beat.
When you win, you get the Earth Element and a heart container. After you have everything, take the green warp and you'll be out of there.
Your next destination is Mt. Crenel.