Three wells have been shown on the Island, although the Man in Black hinted that there were several more. The wells appear to have been created by an ancient civilization and identify the locations of the Island's energy pockets.
From the account told by the Man in Black, the wells were dug by hand by an ancient civilization. These early Island inhabitants were confused as to why their compasses were acting so strangely in proximity to the energy pockets and dug the wells in an attempt to determine the cause. The Man in Black commented further that they learned nothing from their attempts, although this statement is rather at odds with the existence of the frozen wheel chamber. ("Everybody Loves Hugo")
During the early years of Island, the Man in Black lived for many years in a village with Claudia's people. During this time he was instrumental in the digging of at least one of the wells -- wherein he managed to locate an alternate route to the Source. He planned to harness this energy as a means of leaving the Island although was stopped by his mother, who knocked him unconscious. Upon awakening, he found that the well had been collapsed, the village destroyed and his people slain. ("Across the Sea") It is not clear if the collapsed well was the same location as that of the Orchid.
The Orchid well was a structure built in the past that led to the frozen wheel chamber. The well was built by The Man in Black and his people as a way to the light. After Mother found out about the well she quickly filled the well with dirt. At an unknown point in the Island's history, a time-shifting Locke used the well (which had been dug up again) to reach the wheel chamber. During this time, the well was located in a small clearing in the jungle and had a rope descending into the depths. Later in 1974, the time-shifting survivors discovered it had collapsed and was filled in. It was located close to the location of the (future) Orchid station, and at least at some point before the well's construction, the statue of Taweret was clearly visible from that location. At that point, however, the well was completely non-existent for Locke's contemporaries on the surface after he landed in the chamber. Therefore, the well may not have been the original means of accessing the chamber. Furthermore, there seemed to be a time anomaly within it. ("This Place Is Death") ("LaFleur") ("There's No Place Like Home, Part 3")
In 2007, the Man in Black led Desmond to a second crumbling well located in a clearing in the jungle south of his camp. Unlike the well near the Orchid, this one was still intact as of 2007 and did not possess a rope leading down into the depths. ("Everybody Loves Hugo") The well was about 20-30ft deep and was partially full of water. ("The Last Recruit")
After explaining the history of the wells on the Island to Desmond, the Man in Black threw Desmond inside. ("Everybody Loves Hugo") He later sent Sayid there to kill Desmond, but Desmond talked him out of it. ("The Last Recruit") Rose and Bernard helped Desmond out by throwing in a rope. ("What They Died For") ("The End")