The efficient removal of organic contaminants from wastewater is, nowadays, a prominent area of study due to its biological as well as environmental significance. Antibiotics are now found in wastewater because of their high use, which has become a source of aquatic pollution. These antibiotics have dangerous implications for people’s health. Hence, effective pharmaceutical removal from wastewater and contaminated water bodies, especially the removal of antibiotics, is of major interest to global research organizations. This is why it is necessary to investigate this class of toxic material in wastewater discharge. We synthesized three different coordination polymers (CPs) in the presence of various assistant carboxylate linkers, namely, [Zn(Hbtc)(dip)]n (1), [Zn4(1,2-bdc)4(dip)4]n (2), and [Zn(1,4-bdc)(dip)]n (3) (3,5-di(1H-imidazol-1-yl)pyridine = dip, 1,3,5-benzenetricarboxylic acid = H3btc, 1,2-benzenedicarboxylic acid = 1,2-H2bdc, and 1,4-benzendicarboxylic acid = 1,4-bdc). These CPs were characterized by using different techniques, including single-crystal X-ray diffraction. The structural studies demonstrated that in 2, there are four Zn(II) centers and both centers are in different coordination environments (Zn2 has distorted tetrahedral geometry, whereas Zn1, Zn3, and Zn4 have square pyramidal geometry). Hirshfeld surfaces analysis revealed that different types of intermolecular interactions (C⋯C, H⋯C, H⋯H, O⋯C, N⋯H, and O⋯H) are present in the synthesized CPs. We examined the different antibiotics, such as metronidazole (MDZ), nitrofurazone (NFZ), dimetridazole (DTZ), sulfasalazine(SLA), and oxytetracycline (OXY), degradation behaviors of the synthesized CPs, which showed remarkable degradation efficiency. 1 showed photocatalytic behavior toward the NFZ antibiotic in an aqueous media. This study also showed that these catalysts are stable and reusable under mild conditions.