We examined the interactions of water and nitrogen availability by subjecting two Populus clones. Tristis and Eugenei, to five soil moisture and three soil nitrogen levels. Nitrogen application significantly increased net photosynthesis and stomatal conductance of flooded Eugenei and Tristis. The onset of flooding caused partial stomatal closure. Net photosynthesis significantly declined after a longer flooding period. Emergence of adventitious roots on the submerged portions of stems in both clones seemingly helped net photosynthesis fully recover in Eugenei and partially recover in Tristis. Under the progressive drought conditions, stomatal conductance was more sensitive to drought than net photosynthesis in both clones. Addition of nitrogen to progressively drying soil induced more stomatal closure in both clones. The highest water-use efficiency was found on the high-N/severe drought zone for Eugenei, whereas it was found on the high-N/mild to moderate drought zone for Tristis.