A schematic of Washington Square Park from the parks department; this shows planned renovations, including moving the fountain slightly to bring it into line with the Arch, but is very close to the plan of the park as it exists today.
Washington Square Park does not have any obvious signs of the old watercourse. Between the development of the park and the real estate development around it in the 19th century, it's been changed many times from its original form. However the water still has to go somewhere, and today there are three parallel combined sewers (carrying both drainage water and sewage) running east to west: one on the north side of the park (Waverly Place/Washington Square North), in a pipe 4'2" by 4"; another on the south side of the park (West 4th St), 4' by 3'; and one through the middle of the park, with a diameter of 54" (4.5 feet). These are shown on the sewer diagram below; probably all three are brick tunnels, from mid- to late-nineteenth century construction. Which, if any of these, carries the remnants of the Minetta Brook?
Famously, it's known that the water of Minetta Brook can be seen from the surface at a marble fountain in the inner lobby of #2 Fifth Avenue (which is just on the north side of the park-- where Fifth Avenue hits Washington Square North).
However, it seems likely that the fountain is no longer supplied by the historic stream, if it ever was. A 1930 NY Times article told about the exposure of the brook in this fountain, but I suspect whatever supplied it has been replaced by standard NYC water supply water (if it ever was Minetta water, and not just a publicity stunt.)
According to the Native's Guide to New York by Richard Laermer (W. W. Norton & Company, 2002), for example, Minetta Brook "dried up in the mid-1800s" and the 2 Fifth Ave fountain merely "symbolizes" Minetta Brook. (Although the plaque on the fountain says that "A brook winds its erratic way beneath this site," and explains that over time Minetta Brook-- sometimes referred to by its nickname 'Devil's Water'-- "has settled underground.")
Despite the improbability, other walking tours and guidebooks still suggest that the fountain is truly Minetta Brook water. Does anyone know any more about this? Please email me if you know! Also if you have a snapshot of the fountain, I'd love to add that to this post-- email me at firstname.lastname@example.org. Thanks!
I've also been told the stream is visible in a fountain at at 33 Washington Square West, which is at the western edge of the park.
References: Native's Guide to New York: Advice With Attitude for People Who Live Here--And Visitors We Like By Richard Laermer Published by W. W. Norton & Company, 2002