Roots are in the Ancestral Mound, City of Tears, Crystal Peak, Deepnest, Forgotten Crossroads, Greenpath, the Hive, Howling Cliffs, Kingdom's Edge, Queen's Gardens, Resting Grounds, Royal Waterways, the Spirits' Glade and two in the Fungal Wastes. You cannot touch any of them until you have the Dream Nail from the Seer in the Resting Grounds, which is why getting the Dream Nail early saves a lot of backtracking.
Essence from roots is the easy half of the Essence economy. The other half comes from the seven Warrior Dreams and from dream bosses, which are fights rather than collection.
How to collect them
Equip nothing special, just find the root and hit it with the Dream Nail. The Essence orbs scatter across the room and drift away, so move immediately and clear the whole room. If you leave, the root is marked as partially collected and you can return for the rest.
Buy the Whispering Root pin from Iselda for 150 Geo. It marks every root you have discovered on the in-game map, including ones you have not yet drained. On this site, filter the map to the Whispering Roots category. Note that roots are hidden by default here because they clutter the view once you have cleared them.
What you get
Roots give Essence, and Essence buys rewards from the Seer: the Dreamgate at 900, a Pale Ore at 1200, the Awoken Dream Nail at 1800, and a Mask Shard plus her farewell at 2400. The Awoken Dream Nail is required for the Dreamers and the true ending. Roots themselves are worth zero completion percent, so they are a means to an end rather than a checklist item for 112 percent.
All 15 locations by area
Forgotten Crossroads (2)
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Ancestral Mound
Inside the Ancestral Mound above the Snail Shaman. Dream Dialogue speaks of Soul attuned, Spiral focus and Shunned Power.
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Top of the Forgotten Crossroads, below the well
In the topmost Crossroads room, just below the well down from Dirtmouth.
Greenpath (1)
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South Greenpath
In the mossy caverns in the south of Greenpath. One of the richer roots in the game.
Fungal Wastes (2)
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North-west Fungal Wastes, near Fog Canyon
In the room at the Fungal Wastes corner closest to the Fog Canyon and the Teacher's Archives.
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Above the Mantis Village
The room above the Mantis Village entrance holds the smallest root in the game.
City of Tears (1)
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North-west City of Tears
In the north-west streets of the City, below the Storerooms.
Crystal Peak (1)
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North-east Crystal Peak
High in the crystal mines on the east side of the Peak. The smallest haul in Crystal Peak.
Resting Grounds (2)
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Resting Grounds, near the Seer
A short walk from the Seer, in the burial chambers of the Resting Grounds.
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Spirits' Glade
Inside the Glade of Hope, east of the Seer. The Glade opens once the Seer has been given 200 Essence.
Howling Cliffs (1)
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Lower Howling Cliffs, below Cornifer
Down and left from where Cornifer sits on the cliffs.
Royal Waterways (1)
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Broken lift shaft, east Waterways
In the ruined lift shaft that drops from the Waterways toward the Ancient Basin.
Deepnest (1)
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West Deepnest, near the Distant Village
Deep in the dark western half of Deepnest. Bring the Lantern or you will never spot it.
Kingdom's Edge (1)
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West Kingdom's Edge, in the falling ash
Out in the ash on the west side of Kingdom's Edge. This is the richest root in Hallownest.
The Hive (1)
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Central Hive
On one of the wax platforms in the middle of the Hive, past the Hive Soldiers.
Queen's Gardens (1)
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North-east Queen's Gardens
Among the vines in the north-east of the Gardens.