Excess heavy metal concentrations caused by severe anthropogenic activities are among the major threats of aquatic pollution in developing countries like Ethiopia. So far, there is limited information regarding concentrations of selected toxic heavy metals in the freshwater bodies of northern Ethiopian highlands. Therefore, this study aimed to assess the current status and spatial distributions of heavy metals in water and sediment samples of the Megech River located in the North Gondar zone of the Amhara region from November 2018 to January 2019. Six different sampling sites (M1–M6) were identified based on the anthropogenic influence. A total of 30 water and 30 sediment samples were collected along the course of the river. Results revealed that concentrations of Cu (0.11 to 0.17 mg L−1), Zn (0.11 to 0.16 mg L−1) and Cr (0.03–0.05 mg L−1) in the water were within international guidelines for domestic use. In the sediment, maximum concentrations of heavy metals detected at site M2 were within the recommended sediment quality guideline for aquatic systems. Generally, higher concentrations of heavy metals were observed at sites with higher anthropogenic activity (M2). Therefore, continuous monitoring and seasonal studies with representative samples including benthic organisms and macrophytes are needed to quantify the impact on downstream sections.