Understanding the geochemical behavior of the Mo isotopes in estuarine systems is essential for determining the isotopic composition of riverine inputs to the ocean and for assessing the historical oxidation state of Earth’s ancient oceans. However, the extent and mechanisms of Mo isotope fractionation during estuarine processes are not yet fully understood. This study systematically investigated the seasonal and spatial variations in aqueous and particulate δ98Mo values within the Pearl River Estuary (PRE). Our research found that aqueous δ98Moaque. values in both summer and winter deviated significantly from the theoretical mixing line for the PRE. Based on the geochemical characteristics of the water column, particulate matter, and pore water in the PRE, we first propose that diagenesis release from sediments is the predominant factor resulting in lower than anticipated aqueous δ98Moaque. values. Given the prevalence of suboxic and anoxic sediments in estuarine and coastal areas, such diagenetic release may substantially decrease the global riverine influx of aqueous Mo isotopes to the ocean. Additionally, particulate δ98MoSPM values exhibit an increasing trend (from 0.02 to 1.62‰) with increasing salinity in both seasons, suggesting that the terrestrial input particulate δ98MoSPM value would be heavier than the mean value for UCC. We hypothesize that the adsorption and desorption processes involving Fe (hydro) oxides predominantly influence this trend. This study advances our understanding of the mechanisms of aqueous and particulate Mo isotopic fractionation in estuarine systems and would be helpful in constraining Mo isotopic compositions of rivers and oceans.