Geographical:
The relationship of Nephi and Mormon becomes clearer when we look at the geography of highland Guatemala. With the city of Nephi at Kaminaljuyu (Guatemala City), the only body of water in the direction of Zarahemla that could serve as the waters of Mormon was Lake Atitlan. It is about nine by four miles in dimension. Only a sizable lake would do as the Book of Mormon "waters," for two reasons: (1) the same body of water, it appears, later rose enough to submerge the city of Jerusalem (3 Nephi 9:7), a Lamanite center built after Alma's departure, and (2) it was "away joining the borders of Mormon" (Alma 21:1), implying that the two spots were some little distance apart. The distances and directions relating Nephi, Mormon and Jerusalem are appropriate if the latter two were on Lake Atitlan. Nephi at Kaminaljuyu would be approximately 40 air miles from Lake Atitlan" (Sorenson, John L. An Ancient American Setting For The Book Of Mormon. FARMS 1985, page 176 ).
Anthropological: Sorenson takes particular note of the phrase "pure water" that is used to describe the waters of Mormon. He notes that the next community Alma founds is also to be noted for its "pure water" (see Mosiah 23:4). Sorenson suggests that this emphasis is related to a Mesoamerican concern with the waters of the underworld, which were considered sacred (Sorenson 1985, pp. 176-9).
The conception of waters underneath the surface of the earth is widespread. In the Old World it underlay the mythology of Babylon and other Levantine civilizations (see Widengren, Geo. The King and the Tree of Life in Ancient Near Easter Religion. Uppsala: A.-B Lundequistaska Bokhandeln. 1951, p. 35 and Clifford, Richard J. "The Temple and the Holy Mountain." In: The Temple in Antiquity. Religious Studies Center, Brigham Young University, 1984, p. 111). This Levantine conception of the construction of the earth was also adopted by Israel.
John Lundquist expands on the connection between the temple and the waters:
These Ancient Near Eastern conceptions would have blended well with the general water/mountain/temple symbolism of Mesoamerica. This conception of a connection with the "pure" waters of the underworld persists to the Maya present. Note the nature of the water in this description of a modern Maya rite:
Just as this modern "virgin water" came from a deep natural well, there may have been something about the nature of the particular waters that Alma found that he described as "pure waters." They were locations that could be understood to be sacred. Whether drawing upon the more immediate Mesoamerican understanding, or a visceral remembrance of the Old World meanings through the brass plates makes little difference. Alma would easily have understood the sacred relationships of mountains and waters, and founding a religious community in such a sacred place would be more than appropriate, it would be fortuitous.