To clarify the mechanism controlling the migration of uranium and typical heavy metals at the sediment–water interface, four sampling cores were collected along the Mianyuan River near a phosphate mining region to investigate their distribution in pore water and sediment along vertical profiles. This study indicated that: (1) the average concentrations of U, Cd, Cu, Pb, Zn and Ni in the pore water were 2.17, 0.08, 6.28, 1.78, 80.56 and 5.18 µg l−1 , respectively, some of them being higher than the National Recommended Water Quality Criteria. (2) The enrichment of U, Cu, Pb, Zn and Ni in the sediment near the urban area clearly indicated that local industries were important pollution sources. (3) The average diffusive fluxes of U, Cd, Cu, Pb, Zn and Ni of the four profiles were 0.016, 0.007, 0.300, 0.022, 2.925 and −1.328 µg/(m2·d), indicating that most of the metals diffused from the sediment pore water to the overlying water. (4) The IWCTU (Interstitial Water Criteria Toxic Units) values of Pb in the pore water exceeded 1 in most river sections, indicating that the toxicity levels in the sediments presented a risk to aquatic organisms.