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Overview
Access
The Whispering Depths can be accessed from the Blighted Village, via the well located in the centre of the village X: 24 Y: 401, or through the blacksmith's workshop.
Arachnomancer's room
To the west of the well entrance is a small workshopX: -505 Y: -402 (which previously housed a Lolth fanatic. They have left behind four diaries, which describe their "transcendence" into the Phase Spider Matriarch.
Reading all four journals in the room earns the 
Inspirational Event A Solitary Spider (Sage background).
A metal chest beside a writing desk contains the Spiderstep Boots, a gift from Lolth to the arachnomancer.
Centre caves
North of the well is a section of caves with two Phase Spiders and two Ettercaps. There are also some old backpacks with supplies, left by a group of travellers who were trying to return home to the Underdark.
Matriarch's den
At the western end of the depths is a large, open section where the Phase Spider Matriarch can be found.
The Underdark can be accessed by jumping into the central green glowing pit of this room, arriving at an unnamed location dubbed Minotaur Hills at X: 140 Y: -149.
On the western edge of the pit is a 
Dark Amethyst, needed to open the 
Necromancy of Thay. Further west and past the pit is the Whispering Depths waypoint.
Waypoints
This location contains the following waypoint:
Whispering Depths X: -584 Y: -384
Creatures
Notable loot
Notable items obtained in this location, whether looted, purchased, or obtained as a quest reward:
Dark Amethyst a quest item found just beside the central pit in the matriarch's den
Poisoner's Robe looted from the phase spider matriarch
Spiderstep Boots
Spurred Band
Related literature
Related quests
Achievements
Pest Control
Kill the Spider Matriarch before her eggs hatch - why do they have so many legs?