Antibiotics and organic explosives are among the main organic pollutants in wastewater; their detection and removal are quite important but challenging. As a new class of porous materials, metal–organic frameworks (MOFs) are considered as a promising platform for the sensing and adsorption applications. In this work, guided by a topological design approach, two stable isostructural Zr­(IV)-based MOFs, Zr6O4(OH)8(H2O)4(CTTA)8/3 (BUT-12, H3CTTA = 5′-(4-carboxyphenyl)-2′,4′,6′-trimethyl-1,1′:3′,1″-terphenyl-4,4″-dicarboxylic acid) and Zr6O4(OH)8(H2O)4(TTNA)8/3 (BUT-13, H3TTNA = 6,6′,6″-(2,4,6-trimethylbenzene-1,3,5-triyl)­tris­(2-naphthoic acid)) with the the-a topological structure constructed by D 4h 8-connected Zr6 clusters and D 3h 3-connected linkers were designed and synthesized. The two MOFs are highly porous with the Brunauer–Emmett–Teller surface area of 3387 and 3948 m2 g–1, respectively. Particularly, BUT-13 features one of the most porous water-stable MOFs reported so far. Interestingly, these MOFs represent excellent fluorescent properties, which can be efficiently quenched by trace amounts of nitrofurazone (NZF) and nitrofurantoin (NFT) antibiotics as well as 2,4,6-trinitrophenol (TNP) and 4-nitrophenol (4-NP) organic explosives in water solution. They are responsive to NZF and TNP at parts per billion (ppb) levels, which are among the best performing luminescent MOF-based sensing materials. Simultaneously, both MOFs also display high adsorption abilities toward these organic molecules. It was demonstrated that the adsorption plays an important role in the preconcentration of analytes, which can further increase the fluorescent quenching efficiency. These results indicate that BUT-12 and -13 are favorable materials for the simultaneous selective detection and removal of specific antibiotics and organic explosives from water, being potentially useful in monitoring water quality and treating wastewater.