The Crimson Nirnroot, unlike normal Nirnroot, are only found in Blackreach near the giant glowing fungi. Crimson Nirnroot still makes the sound of chimes when the Dragonborn is nearby and has a white glow.
There are at least 44 Crimson Nirnroots in Blackreach so it is not necessary to find them all.
The Crimson Nirnroot glows with a slightly yellow color that can be easily distinguished from the blue glow of the fungi.
While they can be found anywhere on land, Crimson Nirnoot are still found more commonly near water. At least one is found in water, in the central pool of the Derelict Pumphouse. One is found far from water, high up where the frost troll lives.
Turning the audio music off in settings help you hear the "chime" the Nirnroot makes when close by.
To place a Crimson Nirnroot near the player type player.placeatme 000b6fb9 in the console.
Crimson Nirnroots will be removed from your inventory if you eat them, but the quest will not change. It may tell you to return them to the nirnroot farmer in the Rift, but, if you eat any, she will not take them until you have 30.
The quest tracker may not tally all collected Nirnroots properly. This occurs because only one Nirnroot is initially needed, but if more are collected before seeing Avrusa, the others are counted as quest items also.
Alternatively, the above bug can help you receive the Hero of the People Achievement which is to complete 50 Misc. Quests, by storing and retrieving quest items from a chest repeatedly. This also functions for Madesi's quest.
On occasion, the quest system might alert you on having obtained all of the 30 roots when you have less than 30. This may be due to eating multiple Crimson Nirnroots as the game may consider collecting them as picking them while the quest display considers what one has in his inventory.
It may be that if you have collected Crimson Nirnroots before finding Sinderion's Journal those Crimson Nirnroots will not be counted in the quest tracker. Say you have collected 5 Crimson Nirnroots beforehand then you start the quest and collect 20 more, your tally will say 20 but you will have 25. If you try to drop them one by one the tally will go into negatives. Conversely the best way to correct the quest tracker is to offload all your current Crimson Nirnroots into a container or on the floor and pick them up one by one (note, if you have more than 5, and you are given the option to pick up all in one go, then it will still register as only one - you have to pick them up one at a time and wait for the quest tracker to confirm).
If the player collects more than 30 Crimson Nirnroots and deposits the extras in a container before visiting Avrusa Sarethi, the quest update may pop up "Collect Crimson Nirnroot in Blackreach 30/30", indicating that there is in fact 30 Crimson Nirnroots in the player's inventory, but the prompt to see Avrusa Sarethi (and the map marker) is absent. Simply taking another Crimson Nirnroot from the container should fix the problem. (PS3 after 1st update)
Possible but may be that when the player collects all the Crimson Nirnroots and returns to turn in the quest, Avrusa will not have the topic in the conversation window to even ask about Crimson Nirnroots. If this happens, ensure that you actually have 30 Crimson Ninroots and didn't accidentally sell or use one for alchemy. If the player doesn't have 30, they will need to go back to Blackreach and find more. Once 30 Crimson Nirnroots are in the inventory, return to Avrusa and the dialogue option should be there.
For some reason, if you speak to Avrusa about Sinderion's dead body before you show her the Nirnroot, she will stop talking to you altogether and the quest cannot be completed. Make sure to give her the Nirnroots before you tell her of her friend's death. (Fixed on PS3, tested)
360 PS3 If the Crimson Nirnroot is removed from inventory, by placing in a chest or by dropping, one Crimson Nirnroot could subtract several from the Avrusa Sarethi's quest's counter. [E.g. Storing five Crimson Nirnroots in chest at Breezehome subtracted 11 from the total count. So when actually 28 had been collected, the quest counter read 17.] - Additionally, storing or dropping Crimson Ninroot individually will not resolve the problem on the consoles.
360 PS3 By waiting ten game days, the Crimson Ninroot will respawn. You do not need to entirely exit the Blackreach area for this to happen. This can be an easy solution for those having difficulty obtaining the 30 specimens.
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