Per-and poly-fluoroalkyl substances (PFAS) have garnered significant global attention due to their widespread presence and potential environmental and health risks. However, research on the occurrence and environmental behavior of PFAS across different media remains limited. We analyzed the occurrence, distribution, sources, and ecological risks of 32 PFAS across multiple media in the Weihe River, China. The concentrations of PFAS ranged from 5.89 to 472.84 ng/L in the pore water and from 9.93 to 459.50 ng/L in surface water, exhibiting significant spatial variability (P<0.05). In contrast, the PFAS concentration range in the sediments was 0.74-1.81 ng/g dry weight, with no pronounced spatial variation in solid-phase PFAS (P>0.05). Vertically, concentrations in 33.00% of pore water samples exceeded those in surface water, showing a heterogeneous vertical distribution with enrichment at depths of 40-60 cm. The physical-chemical characteristics of PFAS and the hydrological and sedimentary processes at the basin scale were responsible for PFAS partitioning between the aquatic environment and sediments. Four major sources were identified through integrated source apportionment: industrial and domestic wastewater (58.25%), aqueous film-forming foam (18.07%), combined input from household pollution and metal plating (8.70%), and stormwater runoff and landfill leachate (14.98%). The ecological risk assessment revealed negligible risks from short-chain PFAS in surface water and pore water, whereas long-chain PFAS posed low to moderate ecological risks. Furthermore, the discharge of PFAS from the Weihe River to the Yellow River was estimated up to 708.20 kg/a. This study provides critical data informing strategies for mitigating PFAS pollution in rivers across typical arid and semi-arid areas of China.