1670s, lagune, earlier laguna (1610s), "area of marsh or shallow, brackish water beside a sea but separated from it by dunes," from French lagune or directly from Italian laguna "pond, lake," from Latin lacuna "pond, hole," from lacus "pond" (see lake (n.1)). Originally in reference to the region of Venice. The word was applied 1769 (by Capt. Cook) to the lake-like stretch of water enclosed in a South Seas atoll. Also see -oon. Related: Lagoonal.
In regions where Spanish is or formerly was the current language, the word lagoon is likely to be used with more latitude of meaning, since in the Spanish laguna is applied to ordinary lakes, to the bottoms of deep bays, especially when these are more or less closed in by a narrowing of the coast-lines, so as to give rise to lake-like areas, and also to shallow, swampy, or almost dried-up lakes inland as well as near the coast. [Century Dictionary]
There was a Germanic form of the PIE root which yielded Old Norse lögr "sea flood, water," Old English lacu "stream, pool, pond," lagu "sea flood, water, extent of the sea," leccan "to moisten" (see leak (v.)). In Middle English, lake, as a descendant of the Old English word, also could mean "stream; river gully; ditch; marsh; grave; pit of hell," and this might have influenced the form of the borrowed word.