A green, water-based synthesis of thiol-decorated, Zr-carboxylate metal–organic framework is reported. A mixture of capping and bridging, thiol containing, organic linker approach utilizing mercaptoacetic acid (MA) and mercaptosuccinic acid (MSA) resulted in an open Zr-based MOF with thiol-decorated cages (Zr-MSA-MA MOF). Tailoring the nanospace within the micropores of water-synthesized and water-stable MSA-MOF led to several desirable attributes including: (i) chemical stability in aqueous media due to strong –CO2–Zr(iv) linkage, (ii) tight pore system leading to optimized electronic interactions with guest ions, and (iii) thiol-functionalized cages that affect selective capture of soft metal ions. The Zr-MSA-MA MOF demonstrated exceptionally high capacity for Cd (370.4 (±35.5) mg g−1, 3.29 mmol g−1) and Pb (500 (±16.8) mg g−1, 2.41 mmol g−1). It also exhibited remarkable stability indicated by its ability