To evaluate the level of contamination and predict the potential toxicity risk, selected metal concentrations (Cd, Pb, Cr, Mn, Co, Ni, Cu, Zn, and As) were determined in 40 surface sediment samples from the stratified karstic Krka River estuary (Croatia). In addition, diffusive gradients in thin films (DGT) probes were deployed in situ to understand the mobilization mechanisms and bioavailability of metals in the sediment. The results show significant spatial differences between the upper and lower estuary, with the latter being more affected by anthropogenic pollution. The pollution assessment using the enrichment factor (EF), the geoaccumulation index (Igeo), and the pollution load index (PLI) showed a strong enrichment of metals in the lower part of the estuary, especially of Mn, Cu, Zn, Pb, and As. The statistical analysis (PCA) revealed the former ferromanganese factory and the port as major sources of pollution in the area. Nickel, Co, and Cr, although slightly elevated, may be attributed to the natural origin. The metal mobility in the estuarine sediment was primarily governed by early diagenetic processes (aerobic organic matter mineralization, Fe and Mn oxyhydroxide reduction), which caused the release of metals from the sediment into the pore water and subsequently into the overlying water column.