Microplastic (MP) contamination represents an issue of global concern for both aquatic and terrestrial ecosystems, but only in recent years, the study of MPs has been focused on freshwaters. Several monitoring surveys have detected the presence of a wide array of MPs differing in size, shape, and polymer composition in rivers and lakes worldwide. Because of their role of sink for plastic particles, the abundance of MPs was investigated in waters, and deep and shoreline sediments from diverse lakes, confirming the ubiquity of this contamination. Although diverse factors, including those concerning anthropogenic activities and physical characteristics of lakes, have been supposed to affect MP abundances, very few studies have directly addressed these links. Thus, the aim of the present study was to explore the levels of MP contamination in mountain and subalpine lakes from Northern Italy. Fourteen lakes dislocated at different altitudes and characterized by dissimilar anthropic pressures were visited. Lakeshore sediments were collected close to the drift line to assess MPs contamination. Our results showed the presence of MPs in lakeshore sediments from all the lakes, with a mean (± standard deviation) expressed as MPs/Kg dry sediment accounting to 14.42 ± 13.31 (range 1.57–61.53), while expressed as MPs/m2, it was 176.07 ± 172.83 (range 25.00–666.67). The MP abundance measured for Garda Lake was significantly higher compared to all the other ones (F1,13 = 7.344; P < 0.001). The pattern of contamination was dominated by fibers in all the lakes, but they were the main contributors in mountain lakes. These findings showed that the MP abundance varied according to the altitude of the lakes, with higher levels measured in subalpine lakes located at low altitudes and surrounded by populated areas.