While zirconium‐metal–organic frameworks (Zr‐MOFs) show promise for arsenic remediation, their practical implementation faces critical challenges: poor capture of neutral arsenite (H3AsO3 containing As(III)) and limited selectivity for arsenate (HAsO42− and H2AsO4− containing As(V)) species in the presence of competing ions. Here, we present a transformative solution using dimercaptosuccinic acid (DMSA) ligands to construct two topologically distinct Zr‐MOFs. The Zr‐DMSA framework with fcu topology demonstrates exceptional capture of both arsenic species, even in the presence of phosphates, which normally compete for adsorption sites. Through comprehensive structural analysis combining PDF analysis, XAS, and solid‐state NMR, we uncover the molecular basis for this superior performance. Comparative studies with analogous thiol‐free Zr‐MOFs reveal that DMSA's thiol groups enable strong covalent sulfur‐arsenic interactions. Moreover, DFT calculations and XAS analysis illuminate an unexpected mechanism: dangling or flexible DMSA ligands enhance As(III) chelation through rotational freedom that enables effective As‐S bond formation. The remarkable selectivity for arsenate over phosphate likely stems from arsenate's reduction potential, enabling its conversion to As(III) during thiol chelation. This work not only addresses a pressing environmental challenge but also establishes how particle size effects and/or structural disorder, rather than perfect crystallinity, may dramatically enhance MOF performance for selective guest capture.