Playing through the story you will be presented with a choice as to what lead you want to follow up on when you reach the Rosemary and Thyme and speak with a little dwarven friend. Thus, a storyline will be triggered to rescue Dandelion.
Along the way, the best way to get info as to where Dandelion is is to make nice with Djikstra in his broken vault/Whoreson missions.
The mission where you ultimately save Dandelion is "A Poet Under Pressure." You and the dwarf will set up an ambush to spring Dandelion. When you attack the caravan, a Witch Hunter will flee and you must make haste and chase him down to, eventually, a dwarven farm. The Hunter will lock himself and Dandelion in a house and you'll have to get the key to the cellar of the house from the dwarf who lives there. Go into the cellar, kill the Hunter, untie Dandelion and the achievement is yours.
PLEASE NOTE (potential spoilers): This is my first playthrough, I went the route of helping Pricella get Dudu out of hiding and, since I killed the Witch Hunter captain with Triss, I had Dudu impersonate the Captain. I'm not sure if NOT attacking the Witch Hunters straight on with Triss in an earlier mission affects your ability to spring Dandelion or not. If anyone else knows this, please add below so we can make sure I'm either entirely right of if there is an alternative way of saving him.