It has been suggested by some writers that ATCO is an acronym based upon Atlantic Transport Co. If such a company ever existed, it is clear it had nothing to do with the use of "Atco" as the name of this stream and as the name of the town near its head, since the name had been in existence a century before the town of Atco was created by the Richards family (Family Empire in Jersey Iron, p 55); Boyer's Place Names (p 3) suggests the "railroad" may have had some connection with Atsion (which it eventually did) and the author conjures up a mythical Atsion Transport Company.
The earliest spellings suggest they were based on an Indian naming of this important stream. Prowell (p 262) states that Atco was "an Indian term for a place of many deer". It is curious that the 1953 Medford Lakes Quad shows a small tributary of the main stream, wholly within Burlington County and names it Alquatka. It originates in the West Jersey Cranberry Meadow. (See Sign Posts, p 2, where Bisbee spells it Alquatqua.)