I'm writing this walkthrough from the perspective of entering from outside, rather than through the Wolves Den, so if you've entered that way you'll probably find it easier to use the map as well as the walkthrough.
Upon entering you'll have to either light a candle, torch or lamp, or cast the Light spell, if you have a mage in your party. I haven't written down every time you'll run into goblins, because they're scattered through the entire level.
Once you've killed the first few goblins, go towards the south, and down the passage in that direction. There's a few goblins and bats down here, but more importantly, there's a Steel Dagger in a container. This is a good weapon for this early in the game, and you probably want to equip it.
Now go back up to the river and enter the other passage. Once again, when you get the option, go towards the south. You'll get a message about goblins being near. After killing the goblins you'll find an Iron Short Sword on the ground, and some lockpicks in a container.
Now back down to the main passage, and up towards the north. There's some crates with food in them up here, which you might want to pick up.
Now it's time to head down the far southern corner. In the room at the end of the passage you can pick up some potion making herbs before heading through the door. There's a few goblins and a wolf in here. One of the goblins will drop a Bolt of Fire scroll if he hasn't used it on you. You'll find some coins and a curing potion in the chests. Now head out the door to the west, but don't go down the ramp that's right against the wall yet. Go a little to the right and there's a ramp leading down to a locked room. There's a couple chitrach larvae in there, but nothing else.
The next two side passages just lead to the garbage pit, which has a serpent in it, and a room with a couple goblins.
The next passage westwards leads to an area with three locked doors and a chute leading down. The chute just takes you back to the chitrach room. The three locked cells hold a mung rat, a giant lizard, and the body of an Avernum soldier. Nothing much in there.
The last side passage leads to a bridge. Don't forget to pick up the healing herbs on the ground, and there's some food in some pots right before the bridge. Once over the bridge you can go towards the west, but it's just a dead end, and there's nothing there but a bat. Now towards the north, where you'll find the Goblin graveyard and a few rats.
Now up and over another bridge. There's two goblins here, one of whom drops a Bolt of Fire scroll. Through the door is the Goblin temple. Kill all the goblins, and the two skeletal warriors. I've sometimes found a Stone Short Sword+ here, which gives +5% less chance to be hit in combat. It's generally not a good idea to pray at evil altars, but remember it's there for later on in the game, as you can perform the Ritual of Sanctification on it once you get the ability. It gives you 100 experience.
Now head down the passage to the east, into the area where the better goblins live. There's a chest with healing potion. There's also a secret passage in the little alcove near the river. This leads you to a boat. There's some potion making herbs there, and also on the little island right across. Into the boat and down the river. You'll see a little ledge sticking out of the water with some poisonous areas and a pool at the back. You can get a Lightening Spray scroll from the pool.
Now get back in the boat and row under the bridge to get to an area with some mushrooms and a ramp leading down. Follow the ramp down, but there's some Giant Spiders down there. Once you've dealt with them clear all the webs and go down the little alcove. There's another secret entrance here, through which you'll find some more Giant Spiders. Once you've killed them check the ground for a healing potion and a Nature Lore charm. Then check the chest for a Crafted Chain Mail. Once you've gotten that go back to your boat and back to the main area. Go back to the far south, and down the ramp to the Wolves Den.