The extent of microplastic pollution in freshwaters in New York State is largely unknown. Lakes present a challenge for microplastic sampling and study due to seasonal variations in the magnitude of pollution sources. This work expands on prior sampling in Onondaga and Skaneateles lakes in central New York with additional sampling in July and November of 2021 using two sampling methods, pump and net sampling. Water samples were characterized for microplastics using visual ID and subsampled for polymer identification using ATR-FTIR. Pump sampling rarely provided counts exceeding background concentration levels, limiting interpretation of depth sampling. Microplastic concentrations found using net samples varied with time and were typically higher in Onondaga Lake compared to Skaneateles Lake. This work provides further information on the impacts of seasonal stratification on microplastic contamination and variations in the concentrations and types of microplastics among lakes.