The anthropogenic heavy metal dissemination in the natural environment through riverine sediments is a major ecological and public health concern around the world. This study gives insight into the source apportionment and potential ecological and health risks of heavy metals in river sediments of the Urmia Lake basin, a natural world heritage located in northwestern Iran. A comprehensive sediment sampling was conducted in seven major rivers feeding the basin during the summer and winter of 2021. Samples were analyzed for zinc (Zn), copper (Cu), cadmium (Cd), lead (Pb), and nickel (Ni) contents and a suite of chemical and physical properties. Subsequently, Pollution Index (PI), Pollution Load Index (PLI), Ecological Risk (ER), Hazard Quotients (HQ), Hazard Index (HI), and Carcinogenic Risk (CR) indices were determined. The mean concentration of heavy metals in all rivers’ sediments exhibited the descending order of Ni > Zn > Pb > Cu > Cd during both summer and winter. Multivariate analysis suggested that Zn was primarily initiated from natural processes, Cd and Pb were affected by human activities, and Cu along Ni were derived from natural and anthropogenic factors. The PI unveiled that most sediment samples were unpolluted to slightly polluted by Zn, Cu, and Pb, and slightly to moderately polluted by Cd. PLI and ER indices demonstrated that the sediment poses non to moderate pollution and low to moderate ecological risk, respectively. Using a human health risk approach, we found that the HI values of all heavy metals and THI were less than one for children and adults implying non-carcinogenic risk in the analyzed sediments. Carcinogenic effects of Cd and Pb at all rivers sediments via ingestion, inhalation, and dermal contact were almost within tolerable risks (1 × 10−6 to 1 × 10−4) for children and adults. PI, PLI, ER, HQ, HI, and CR index values of sediment samples during the summer were higher than those during the winter. This is attributed to the greater heavy metal concentrations and the lower water flow during summer. Our results provide practical information for better management and control of heavy metal pollution in aquatic-sedimentary ecosystems.