Q. We often refer to Chesapeake Bay as “the bay” on second mention (e.g., Chesapeake Bay is one of the largest estuaries in the world; we often visit the bay to conduct trawl surveys). My question is whether it is correct.

A. Chicago style lowercases “the bay” as you do, but uppercasing it is not incorrect, and you are likely to see it capped in various publications.