Description: The development of stable barium (Ba) isotope measurements provides a novel tool to investigate the geochemical cycling of Ba in the ocean and its sediments. In sediment pore waters, gradients of dissolved Ba concentrations result from various diagenetic processes. The distribution and fractionation of Ba isotopes in the pore waters are expected to further improve our understanding of these early diagenetic control mechanisms. Here, we present pore water profiles of dissolved stable Ba isotopic signatures (δ138Bapw) from shallow water sediments covering the entire Pearl River Estuary (PRE) in Southern China. We find pronounced depth-dependent Ba isotope variations generally showing a shift from heavy to light δ138Bapw signatures from the sediment surface down to 15 cm depth. These gradients are well reproduced by a diffusion-reaction model, which generates an apparent fractionation factor (138ε) of −0.60 ± 0.10‰ pointing to preferential removal of low-mass Ba isotopes from the pore water during solution-solid phase interactions. Consequently, the combined diagenetic processes induce the highest δ138Bapw values of +0.5 to +0.7‰ in the pore waters of the topmost sediment layer. Although the detrital fraction dominates the Ba content in the PRE surface sediments, the determined gradients of pore water Ba isotopes, together with concentration variations of Ba and other redox-sensitive elements such as manganese (Mn), show that non-detrital excess Ba carriers including Mn oxides and authigenic barite clearly affect the post-depositional Ba dynamics. Stable Ba isotopes are thus a potentially powerful tracer of Ba geochemistry during early sediment diagenesis in estuarine depositional environments. Key Points We present a data set of dissolved stable Ba isotopic compositions in surface sediment pore waters of a large river estuary Pore water Ba isotope values generally decrease with increasing sediment depth, reflecting post-depositional Ba isotope fractionation A diffusion-reaction model predicts the distribution and fractionation of stable Ba isotopes in the sediment pore waters well