Microplastics (MPs) are emerging contaminants in agricultural regions owing to the widespread use of plastics in farming activities. Groundwater has a vital role in farming activities, and it can be contaminated by MPs, fragmented from plastic products used in agricultural activities. Following an appropriate sampling protocol, this study investigated the distribution of MPs in shallow to deep aquifers (well depths: 3–120 m) and cave water of an agricultural region in Korea. Our investigation found that MPs contamination can penetrate up to the deep bedrock aquifer. The abundance of MPs was lower during the wet season (0.014–0.554 particles/L) than during the dry season (0.042–1.026 particles/L), which may be attributed to the dilution effect of precipitation in the groundwater. The abundance of MPs increased as the MPs size decreased at all sampling points, and size ranges were 20.3–869.6 and 20.3–673.0 μm in the dry and wet seasons, respectively. Our findings showed lower MPs abundance compared to previous studies, and we inferred that it might be due to differences in groundwater sampling volume, low agricultural intensity, and the non-application of sludge fertilizers. Our findings suggest that repeated and long-term investigations are needed to identify better the factors that influence the results of MPs distribution in groundwater, including sampling methods and hydrogeological and hydrological conditions.