Many of the desirable properties of metal-organic frameworks (MOFs) can be tuned by chemical functionalization of the organic ligands that connect their metal clusters into multidimensional network solids. When these linker molecules are intrinsically fluorescent, they can pass on this property to the resultant MOF, potentially generating solid-state sensors, as analytes can be bound within their porous interiors. Herein, we report the synthesis of a series of 14 interpenetrated Zr and Hf MOFs linked by functionalized 4,4'-[1,4-phenylene-bis(ethyne-2,1-diyl)]-dibenzoate (peb(2)-) ligands, and we analyze the effect of functional group incorporation on their structures and properties. Addition of methyl, fluoro, naphthyl, and benzothiadiazolyl units does not affect the underlying topology, but induces subtle structural changes, such as ligand rotation, and mediates host-guest interactions. Further, we demonstrate that solid-state photoluminescence spectroscopy can be used to probe these effects. For instance, introduction of naphthyl and benzothiadiazolyl units yields MOFs that can act as stable fluorescent water sensors, a dimethyl modified MOF exhibits a temperature dependent phase change controlled by steric clashes between interpenetrated nets, and a tetrafluorinated analogue is found to be superhydrophobic despite only partial fluorination of its organic backbone. These subtle changes in ligand structure coupled with the consistent framework topology give rise to a series of MOFs with a remarkable range of physical properties that are not observed with the ligands alone.