Mercury (Hg) concentrations in freshwater fish across the state of New York frequently exceed guidelines considered harmful to humans and wildlife, but statewide distribution and temporal changes are not well known for the state’s streams and rivers. We analyzed existing data to describe recent spatial patterns and identify key environmental drivers of these patterns. Size classes within sportfishes and prey fishes formed ‘functional taxa’ (FT), and standardized scores were generated from 2007-2016 data for 218 sites. Muscle Hg in >1 sportfish FT exceeded human-health guidelines of 50 ng/g (sensitive populations) and 300 ng/g (general population, GP) at 93% and 56% of sites, respectively, but exceeded 1000 ng/g (a state threshold) at only 10% of sites. Whole-body Hg in >1 prey fish FT exceeded wildlife thresholds of 40 ng/g and 100 ng/g at 91% and 51% of sites, respectively. Environmental drivers of recent spatial patterns include extent of forest cover and storage, the latter an indicator of wetlands. Standardized Hg scores increased with increasing atmospheric Hg deposition and storage across rural ‘upland’ regions of New York. However, scores were not related to atmospheric deposition in more-developed ‘lowland’ regions due to the limited methylation potential of urban landscapes. Some recent stream and river fish Hg spatial patterns differed from those of lake-based studies, highlighting the importance of New York’s flowing waters to future Hg monitoring and risk assessment.