Microplastic (MP) pollution has become a significant environmental concern, particularly in freshwater systems. However, little is known about the occurrence and characteristics of MPs in groundwater-fed freshwater sources such as natural springs. In this study, the presence, abundance and characteristics of MPs were investigated in freshwater natural springs across South Africa, representing different land-use types (i.e. rural and peri-urbanl) and spring type (i.e. modified and unmodified). On average, 6 particles per L (± 1.2 SD) of MPs were recorded, ranging between 2 (limit of quantification; LOQ) to 38 particles per L. Land-use and spring type did not show any significant influence on MPs abundance (p > 0.05). Overall, MPs exhibited diverse characteristics. Fibres (67.8%) were the predominant shape, while blue (28.8%) was the most common colour. The dominant size class was 100–250 µm across all springs, while the dominant polymer was polyethylene (PE; 46.8%). Our findings suggests that groundwater-fed water sources like natural springs, regardless of their limited exposure to above ground environment, are equally at risk of MPs contamination, similar to surface freshwater systems. This research provides empirical evidence on MPs contamination and monitoring of remote ecosystems, highlighting the ecological and social risk of MPs pollution in important freshwater resources. The study contributes valuable data for understanding MP dynamics including their densities and sources from groundwater-fed freshwater resources, offering insights into broader environmental pollution to African systems.