During the Bassett Creek Tunnel survey of 1993 numerous creatures were noted, but it was not the ordinary life of streams or caves.  For example, there was a pool about midway through the tunnel that was full of goldfish (see photo).  A (dead) garter snake, obviously washed in, was found draped over one of the driftwood dams that so impeded exploration in the pre-diversion era.  Large white mushrooms were seen growing from crevices in the walls, like sconce lamps. There was the occasional sandbar, located in a favorable sunspot under a grating, that was covered with seedlings. In the "Egyptian Gallery" near the outfall bats were observed, but I was not able to identify the species in the murk.  The most "normal" fauna exists near the outfall, where the tunnel is essentially just a backwater of the Mississippi River, and there are numerous carp, clams, etc.  It may be that the Manhattan sewers are full of alligators, but none were found in the Bassett Creek Tunnel!
The Bassett Creek goldfish