The disrupted ecology of metropolitan areas, including microscopic and cryptic communities, must be assessed for purposes of sustainability. Therefore we sequenced 16S rRNA, 18S rRNA, and COI amplicons from 25 river sediment and 23 river surface water samples, collected in 2015 and 2016, from the historically degraded but recovering Hunts Point Riverside and Soundview Parks in the Bronx River Estuary, New York City.