The global issue of heavy metal pollution in surface water poses a significant concern, with the potential to harm public health through various pathways. Given that pollution levels are dependent on water bodies and seasons and their potential impacts on human health vary with children and adults, it is crucial to identify and quantify pollution sources for the development of sustainable management strategies. The current study aimed to evaluate pollution levels and associated health risks of heavy metals and to quantify their pollution sources in various surface water bodies in Khanh Hoa, Vietnam. Water samples were taken from three water bodies (reservoirs, rivers, and narrow waterways) during two seasons (dry and rainy) from 2016 to 2020 and analyzed for seven heavy metals. The results showed that iron had the highest concentration of 392.4 (μg L−1), followed by zinc (25.7 μg L−1), arsenic (3.93 μg L−1), copper (3.77 μg L−1), lead (2.77 μg L−1), chromium (2.71 μg L−1), and cadmium (0.57 μg L−1). Narrow waterways were more polluted with heavy metals (heavy metal pollution index, HPI = 29.5) than other water bodies, such as rivers (23.3) and reservoirs (21.7), and the dry season had a higher HPI (26.5) than the rainy season (24.0). The hazard index for children varied from 1.2 to 1.48, while that for adults was less than 1, suggesting that surface water may have adverse impacts on children's health. The factor analysis identified three primary sources of contamination, namely combustion emissions/street dust, agricultural run-off, and other sources. Cadmium is the most critical metal in determining HPI, while arsenic and chromium are the two key elements potentially influencing children's health. Managing pollution sources, reducing the metal concentration, and controlling the pathways through which metals enter the human body should be implemented for a healthier environment and long-term development.