Microplastic (<5 mm) pollution is a globally recognized problem which varies regionally. Freshwater ecosystems have been vastly overlooked and under characterized for microplastics, including those in central New York. We provide the first measurements of suspected microplastic abundance and form in the surface waters of Onondaga Lake and its tributaries, as well as in the relatively pristine Skaneateles Lake. We found that samples from Onondaga Lake had higher concentrations than Skaneateles Lake, likely owing to more prevalent sources of plastic pollution from litter, wastewater effluent, combined sewer overflows (CSOs), and others. Our methodological development found that microplastic concentrations are highly influenced by sampling methodology, with lower concentrations but greater morphological diversity found in net samples compared to lower volume grab samples. Our findings indicate that microfiber pollution is the primary source of microplastics to these freshwater ecosystems. We also observed that, despite a ban on rinse-off cosmetics in 2015, samples from Onondaga Lake contained microbeads. Our work suggests the need for further improvements to policies addressing microplastic pollution in New York State and has important implications given the use of Skaneateles Lake as the primary drinking water source for the City of Syracuse.