by day: during the daylight hours, as opposed to the night
This is a small, fixed word that answers the question "when?" with "in the daytime." It is built from the ordinary word for "day," but unlike that noun it is not counting calendar days or naming a date. It simply marks that something happens while it is light out.
Its most natural home is alongside its partner "night." Sometimes the two are kept apart, so that day and night each get their own event: a cloud leads Israel by day and a fire by night, or a thief hides by day and digs through houses after dark. There the word means exactly what it says, daytime over against nighttime.
Very often, though, "by day and by night" is welded into a single phrase that no longer divides the clock into two halves. The pair becomes a way of saying "all the time, without a break": one is to study God's instruction day and night, the temple gates stand open day and night, the mourner weeps day and night. The word has not changed its meaning; the phrase as a whole simply reaches for totality.
In two verses in Jeremiah the form is used in an unusual way, not as the adverb "by day" but almost as a noun, "the daytime" itself, set in parallel with "the night" as the thing God has bound by covenant. The daylight in view is the same; only the grammar shifts.