Microplastic pollution (plastic particles < 5 mm) has potentially harmful impacts on aquatic ecosystems. Understanding the factors that impact microplastic loading and distribution within aquatic ecosystems is crucial for assessing potential threats from microplastics. Here we examine the extent of microplastic pollution in the surface waters and sediments of four small inland lakes in Minnesota, USA that represent a range of human impacts as well as a variety of watershed and lake characteristics. Surface water particulates and benthic sediments were collected in the summers of 2019 and 2020 to examine the loading of microplastics into these lakes and their distribution throughout the ecosystems. Lower size cut offs were set at 330 μm for surface water particulate samples and 250 μm for sediment samples. Watershed to surface area ratio (WS:SA) and urban development were the most influential factors on microplastic loading. Surface water microplastic concentrations ranged from 27,000 microplastics km−2 in Elk Lake (small WS:SA and minimally developed) to 152,000 microplastics km−2 in White Iron Lake (large WS:SA and low development). Concentrations in benthic sediments ranged from 30 microplastics kg−1 dry sediment in White Iron Lake (forested watershed) to 270 microplastics kg−1 dry sediment in Peltier Lake (urbanized watershed) and were not directly correlated to surface water concentrations. Results from this study highlight the characteristics of small lakes that influence spatial and temporal variability in microplastic loading, retention, and deposition of microplastics to sediments. Further, this study demonstrates the difficulties of accurately predicting microplastic loading and the importance of comprehensive sampling to account for the variability of microplastic loading and distribution in smaller inland lakes.