Unlike all other plants in the game, Nirnroot does not regrow; each plant can only be harvested once. Consequently, Nirnroot is a rare plant—so rare, in fact, that no alchemist recognizes what the plant is except a man named Sinderion, located in the basement of the West Weald Inn in Skingrad.
Most Nirnroots are found near bodies of water, some are found in various buildings throughout Cyrodiil. Paying attention to shorelines and potted plants while traveling helps locate these plants without extra effort. A faint, pulsating sound emits from the location of a Nirnroot.
Speak to Sinderion in the basement of the West Weald Inn in Skingrad, or harvest Nirnroot for the first time then speak to any alchemist to learn Sinderions location. After collecting enough Nirnroot, Sinderion will create an Elixir of Exploration with increasing degrees of strength. He will then sell them to the Champion at a discount, as well as give them one for free.
Go inside Imperial City Sewers – North Exit and enter the first door to the right. Initially this door is blocked but it can be opened by turning the wheel inside the adjacent chamber. The Nirnroot is to the right from the entrance, in the water next to small stairs.
Under the water where the Sacred Lotus plants are in the Temple District.
In the Waterfront District, at the north end of the docks on the beach near the pirate's ship, named The Marie Elena. There is another one inside the ship itself in a planter on the desk near the entrance of the ship, but the pirates may become hostile if boarded. The third is at the far southeast end of the small island.
Generally speaking, one can walk or ride along any major or minor body of water and find Nirnroot growing. Sometimes they grow between rocks or behind trees, and so require a bit of searching, but most often they are found relatively out in the open. Traveling along the Niben between Leyawiin and Bravil will yield quite a few Nirnroot.
Along the southern beach of Topal Bay, west of the Niben River, in extreme southern Cyrodiil.
South of Bogwater camp in southern Cyrodiil, along the beach.
On island southeast of Bogwater camp.
On an island connected to the mainland by a bridge slightly southwest of Bogwater camp.
West of that same bridge, along the coast.
In the wilderness, southeast of Bravil, south of Fort Irony. It is on the southern edge of the peninsula. Follow the coast until a derelict, burnt-out house on a small island is reached; it is connected to the mainland via a bridge. One Nirnroot is on the island. Another sits immediately north of the bridge.
On the north side of Fort Irony.
About halfway between Fort Redman and Fort Irony, between Leyawiin and Bravil. It's on an island north of a bridge crossing the river (the map shows it's a peninsula, but it is in fact an island).
Across the river of Fort Redman.
On the water's edge of the southern inlet, due north of Leyawiin, southeast of Bravil.
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