The poem's metaphors and similes help illustrate the eerie mysteries of "well[s]," "the sea," and "nature."
First, the speaker compares well water to an otherworldly creature in a remote container:
A neighbor from another world
Residing in a jar
Whose limit none have ever seen,
But just his lid of glass -
The "lid of glass" refers to the glassy surface of the water (here imagined as the top of the "jar" the water "Resid[es]" in). The speaker then compares this watery surface to the "face" of an "abyss"—meaning a huge void or pit. (Or, in some contexts, the pit of hell!) Both the metaphor and the simile depict the water at the bottom of the well as remote, alien, intriguing, and frightening.
Later, the speaker describes the "sea" as "floorless," meaning that it has no bottom. (Or none that people can reach and live to tell the tale. In Dickinson's day, submarine technology was in its infancy, and humans could not yet explore the deepest parts of the oceans.) Just as the previous metaphors evoked the scary, disorienting depths that open up under the earth, this metaphor evokes the scary, uncharted depths that lurk under the sea.
Later, the metaphors in lines 17-20 cast all of "nature" in the same spooky light:
But nature is a stranger yet;
The ones that cite her most
Have never passed her haunted house,
Nor simplified her ghost.
In other words, just as a "ghost" inhabits a "haunted house," some dangerous, alien power seems to inhabit all of nature. Humans who think they understand this power ("The ones that cite" it confidently) are fooling themselves. Nature can't be "simplified" into some tidy explanation; in fact, humanity can barely begin to understand it at all.