In the mid-2000s a survey was conducted to evaluate fish mercury in lakes across New York State. Approximately 10 years later a second survey examining adult sportfish from 103 lakes and reservoirs was conducted to evaluate the response of fish mercury to recent declines in US mercury emissions. Of those lakes, 43 were part of the earlier survey and were examined to determine if mercury concentrations in four popular sport species, Yellow Perch, Walleye, and Small- and Largemouth Bass, declined in response to decreasing emissions. Water samples were also collected at 35 of these lakes and analyzed for mercury, methylmercury and other analytes. The Adirondack and Catskill regions remain biological mercury hotspots with elevated concentrations in fish. The most widely sampled species, Yellow Perch, showed significant increases in mercury in the Northeast and West regions of New York State over the past decade. The increases in Yellow Perch mercury is not consistent with significant reductions in water concentrations of both total and methylmercury observed corresponding in lake water samples. This discrepancy suggests watershed and in-lake processes beyond mercury emissions, such as recovery from acid deposition, impacts from climate change, or changes in food web structure may be controlling fish mercury concentrations. These results demonstrate a need for a consistent, long-term program to monitor fish mercury to inform the status of mercury contamination in New York State.