Rivers are the natural drainage system, transporting anthropogenic wastes and pollution, including microplastics (plastic < 5 mm). In a riverine system, microplastics can enter from different sources, and have spatial variance in concentration, physical and chemical properties, and imposed risk to the ecosystem. This pilot study presents an examination of microplastics in water and sediment samples using a single sample collection from the rural Raquette River, NY to evaluate a hypothesis that distinct locations of the river, such as downstream of a wastewater treatment plant, upstream of a hydro-dam, and river confluence, may be locations of higher microplastics concentration. In general, our results revealed the presence of high microplastic concentrations downstream of the wastewater treatment plant (in sediments), upstream of the hydro dam (both water and sediment), and in the river confluence (water sample), compared to other study sites. Moreover, the risk assessment indicates that even in a rural river with most of its drainage basin comprising forested and agricultural land, water, and sediment samples at all three locations are polluted with microplastics (pollution load index, PLI > 1; PLIzone = 1.87 and 1.68 for water and sediment samples respectively), with risk categories between Levels I and IV (“minor” to “danger”). Overall, the river stands in a “considerable” risk category (PRIzone = 134 and 113 for water and sediment samples respectively). The overall objective of this pilot study was to evaluate our hypothesis and advance our understanding of microplastic dynamics in rural river systems, elucidating their introduction from a point source (wastewater treatment plant), transit through an impediment (hydro-dam), and release into a vital transboundary river (confluence of Raquette-St. Lawrence Rivers).