Geographic: Sorenson suggests that Jerusalem was located on the more southern shore of Lake Atitlan, which he has identified as the Waters of Mormon:
“When the original missionary band split up, Aaron went directly to a land called Jerusalem, “away joining the borders of [what Alma had called] Mormon” (Alma 21:1). Nephite dissidents had led the Lamanites in building “a great city” there. (The place had been founded not long before; here is another case where the status of “great city” did not refer to the duration or size of a settlement but to its concept and layout.)
….Let us recall that this Jerusalem was covered by waters at the time of the Savior’s crucifixion (3 Nephi 9:7). Now, the level of Lake Atitlan has shifted dramatically—by as much as 60 feet within historical times, and up to 15 feet in a single year—so a city located on this shore could understandably be submerged quite abruptly. So several interesting and plausible reasons lead to our locating Jerusalem at this site” (Sorenson 1985, pp. 223-4.)