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Flooding can adversely worsen metal-contaminated soil and influence phytoremediation efficiency; thus, it is crucial to explore the eco-physiological responses of plants to the combined stress of metals and flooding. Here, the plant growth, photosynthesis, and nutrient composition in the arbor willow (<i>Salix jiangsuensis</i> ‘J172’) and shrub willow (<i>Salix integra</i> ‘Yizhibi’) were studied using a pot experiment with Cu-contaminated soil (239.5 mg<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mo>·</mo></semantics></math></inline-formula>kg⁻¹) under flooded versus non-flooded conditions. <i>S. integra</i> showed a larger bioconcentration factor (BCF) than <i>S. jiangsuensis</i> in both treatments. Flooding markedly decreased the BCFs while obviously increasing the translocation factor in the two willows (<i>p</i><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mo><</mo></semantics></math></inline-formula> 0.05). Flooding enhanced the leaf C:P and N:P ratios while significantly decreased root C:P and N:P ratios, compared to the non-flooded condition. The shrub willow exhibited better tolerance to flooding, with little alteration in biomass and photosynthetic rate, and showed greater potential Cu accumulation capacity, even though its total biomass was significantly lower than that of the arbor willow. Our study also helps further understanding of nutrient balance and stoichiometry of willows in response to flooding and Cu contamination, promoting the management of Cu-contaminated flooded soils.