Co-contamination of ciprofloxacin (CIP) and Cu(II) is common in marine aquaculture water. However, the transmission and transformation of these substances in natural water matrices are often overlooked. This study sought to assess the impact of Cu(II) on CIP degradation in distilled (DI) and simulated (SI) mariculture water, as well as to develop a relationship between Cu(II), CIP, and its degradation products. First, complexation assays and analog computations revealed that Cu (II) forms complexes by binding to the oxygen atoms of the carbonyl (C=O) and carboxyl (COOH) groups in the CIP molecule. Second, photodegradation experiments showed that Cu(II) significantly hindered the degradation effect of CIP in DI water, while Cu(II) did not significantly hinder the degradation of CIP in SI water. Furthermore, the effect of Cu(II) on the degradation mechanism of CIP was determined by combining quenching and EPR experiments, Materials Studio software calculations, and UPLC-MS results. It was demonstrated that Cu(II) enhanced the production of singlet oxygen (1O2), hydroxyl radicals (•OH), and superoxide radicals (•O2−) in DI water. In the presence of Cu(II), CIP undergoes hydroxylation and decarbonylation reactions, forming hydroxylated and nitroxylated products. Additionally, direct defluorination and cleavage of the piperazine ring occur, followed by complexation reactions with Cu(II). However, in SI water, the production of 1O2 depends on the indirect action of Cu(II) and the excited state transformation of organic matter. Experimental evidence has shown that CIP can create intermediate compounds that include O-O peroxide rings, with or without the presence of Cu(II). When Cu(II) is present, the cyclopropyl group of the CIP molecule is more prone to transformation and so degradation. Finally, the toxicity assessment results indicated that both Cu(II) and SI water increased the toxicity of the degradation products.
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