A serie of novel square pyramidal copper(II) complexes [Cu(L)₂H₂O] (3a–d) with O,O-bidentate ligands [L = ethyl-2-hydroxy-4-aryl-4-oxo-2-butenoate; aryl = 3-methoxyphenyl-2a, (E)-2-phenylvinyl-2b, (E)-2-(4′-hydroxy-3′-methoxyphenyl)vinyl-2c, 3-nitrophenyl-2d, 2-thienyl-2e] were synthesized and characterized by spectral (UV-Vis, IR, ESI-MS and EPR), elemental and X-ray analysis. The antimicrobial activity was estimated by the determination of the minimal inhibitory concentration (MIC) using the broth microdilution method. The most active antibacterial compounds were 3c and 3d, while the best antifungal activity was showed by complexes 3b and 3e. The lowest MIC value (0.048 mg mL⁻¹) was measured for 3c against Proteus mirabilis. The cytotoxic activity was tested using the MTT method on human epithelial carcinoma HeLa cells, human lung carcinoma A549 cells and human colon carcinoma LS174 cells. All complexes showed extremely better cytotoxic activity compared to cisplatin at all tested concentrations. Compound 3d expressed the best activity against all tested cell lines with IC₅₀ values ranging from 7.45 to 7.91 μg mL⁻¹. The type of cell death and the impact on the cell cycle for 3d and 3e were evaluated by flow cytometry. Both compounds induced apoptosis and S phase cell cycle arrest. The interactions between selected complexes (3d and 3e) and CT-DNA or bovine serum albumin (BSA) were investigated by the fluorescence spectroscopic method. Competitive experiments with ethidium bromide (EB) indicated that 3d and 3e have a propensity to displace EB from the EB–DNA complex through intercalation suggesting strong competition with EB [K_sv = (1.4 ± 0.2) and (2.9 ± 0.1) × 10⁴ M⁻¹, respectively]. K_sv values indicate that these complexes bind to DNA covalently and non-covalently. The achieved results in the fluorescence titration of BSA with 3d and 3e [K_a = (2.9 ± 0.2) × 10⁶ and (2.5 ± 0.2) × 10⁵ M, respectively] showed that the fluorescence quenching of BSA is a result of the formation of the 3d– and 3e–BSA complexes. The obtained K_a values are high enough to ensure that a significant amount of 3d and 3e gets transported and distributed through the cells.