<p>Trace metal contamination of fish poses one of the most critical environmental and health concerns. Although the extent of contamination of aquatic resources in Bangladesh’s Kaptai Lake is unknown, the levels of ten trace metals (As, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Se, and Zn) in three commercially important small indigenous fish species (SIS), mola (<i>Amblypharyngodon mola</i>), kaski (<i>Corica soborna</i>), and chapila (<i>Gudusia chapra</i>), were investigated between the dry and rainy seasons. The concentrations of trace metals from SIS were determined using the energy-dispersive X-ray fluorescence system (EDXRF) and implications for evaluating human health risks. The present study shows that all trace metals differed significantly (<i>p</i> &lt; 0.05) among the species and locations except Ni (0.15–0.77&#xa0;mg/kg) and Se (0.40–1.49&#xa0;mg/kg) between the dry season and the rainy season. Toxic metals (Cr, Cu, and Zn) in mola, kaski, and chapila had significantly (<i>p</i> &lt; 0.05) higher concentrations than the recommended guideline values. The total hazard quotient (THQ) displayed that the non-carcinogenic effect was lower as observed in both children and adults, with the rainy season reflecting more non-carcinogenic risks than the dry season. The hazard index (HI) value for SIS in both seasons (8.66–71.80 × 10⁰) was substantially higher than the recommended threshold (&lt; 1), suggesting a higher potential non-carcinogenic effect on both children and adults. The results also reveal that children (3.92 × 10⁻³–6.63 × 10⁻⁴) are more vulnerable to carcinogenic risks in As and Cr levels than adults (1.06 × 10⁻³–9.05 × 10⁻³), implying that eating these SIS has a greater carcinogenic impact in both dry and rainy seasons. To ensure the sustainable use of aquatic resources in this artificial lake, strict regulations and monitoring may be required to limit the accumulation of hazardous metals in fish.</p>