In situ monitoring of Sb speciation improves the understanding of Sb biogeochemistry and toxicity in ecosystems. Precise measurement of Sb is a challenge due to its instability of oxidation and ultra-trace concentration. The development of simple and reliable methods specific to SbIII measurement is not only appealing but essential for implementing regulations. Here, we present an in situ speciation analysis method for SbIII, using the diffusive gradients in thin films (DGT) technique, combined with mercapto functionalized SBA-15 mesoporous silica nanoparticles (MSBA). Laboratory performance tests confirmed MSBA–DGT uptake was independent of pH (4–9) and ionic strength (0.1–200 mmol L–1). DGT devices equipped with MSBA-based binding gels showed a theoretically linear accumulation of SbIII and exhibited high capacity for SbIII at 65 μg per gel disc, with negligible accumulation of SbV over a 72 h deployment. Compared with commercial 3-Mercaptopropyl functionalized silica (MFS), the nano-sized MSBA facilitate its even distribution in the binding gels. Furthermore, the good selectivity and high homogeneity of the MSBA gel enabled it to be applied in a rice rhizosphere in conjunction with AgI gel to investigate the effects of sulfur application on the SbIII solubility. In summary, the newly developed MSBA–DGT provides a selective measurement of SbIII, showing potential for environmental monitoring and further application in understanding biogeochemical process of Sb.