Histopathology is currently being used as a screening method to detect copper toxicity in fish. However, a knowledge gap exists regarding copper’s effects on the gill epithelial ultrastructure. To fill in this gap, Nile tilapia Oreochromis niloticus were acutely exposed to sublethal and lethal waterborne copper concentrations. Results showed that in the basal region of gill lamellae, a sublethal concentration caused edema, stretching of pillar cells (PLCs), and the disappearance of pericytes (PCTs), whereas in the apical region PLCs remained intact, and PCTs and pavement cells (PVCs) were activated. In the filament epithelium, PVCs showed structural signs of high functional activity, while mitochondrion-rich and mucous cells were degenerated. In the deep filament region, there were edema, loss of neuroepithelial cells, proliferation of undifferentiated cells (UDCs), and transformation of leukocyte-like cells into macrophages. Acclimation was characterized by vasodilatation of the entire lamellar axis and a decrease in the filament epithelial thickness. The protruding lamellae showed PCT proliferation, whereas the superficial filament epithelium became denser due to UDC attachment. All fish exposed to the lethal dose died within 24 h. Gills showed vasodilatation and edema that had lifted the PVCs, and necrosis was evident. In conclusion, our findings contribute to clarification of gill epithelial cell dynamics, and also revealed that apical and basal regions of the lamellae showed different responses, with the apical region exhibiting higher resistance to the toxic actions of copper. Also, superficial and deep regions of the filament epithelium showed dissimilar responses to copper, with the deep epithelium playing important roles in regeneration and protection.