Fish mercury (Hg) data were compiled for 392 unique locations on freshwater streams and rivers in New York State for the period 1969-2016. A total of 7620 records were compiled from state, federal, and non-governmental organization databases. The compiled data were for samples of 65 non-anadromous species or species groups in which Hg was analyzed in whole fish or edible flesh, and for which sufficient ancillary data were available for interpretation. This data release provides total Hg concentrations on a wet weight basis, ancillary sample data (e.g., fish length, body part analyzed), collection location information (description, latitude, longitude), and source of original data. The data release also contains environmental data for selected sites that were sampled during 2007-16. These environmental data include watershed characteristics, site elevation, ecoregion location of the site, and atmospheric Hg dry, wet, and total deposition flux estimates for March through November 2010.