From Old Wells and Watercourses of the Island of Manhattan, by George Everett Hill and George E. Waring, Jr. in Historic New York: the First Series of the Half Moon Papers (New York, 1899):
The Canal Street stream was apparently large enough that prior to the european settlements, the natives of the region could canoe (at least at high tide) from the Hudson river, along the stream, and into the Collect Pond, carrying deliveries of oysters that would be opened and dried for winter food. According to Old Wells and Watercourses..., this helped create the huge mounds of shells that the Dutch found around the Collect pond. This led to it being called "Kalch Hoek," meaning Shell Point, which was probably corrupted into "Collect" later.
A 1766 map showing the line of the drainage canal and the surrounding marsh (close-up view first; second image is entire map):