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In 2019, the Mississippi River watershed had a record-long flooding, which was comparable with the 1927 Great Mississippi River Flood. This study leveraged this flooded condition to assess the flood tolerance of eastern cottonwood (Populus deltoides) and black willow (Salix nigra) planted as short rotation woody crops (SRWCs) on seasonally flooded marginal land of the Lower Mississippi Alluvial Valley (LMAV) in 2018. The survival/mortality prediction models developed by using hydrologic and environmental variables suggested that only high flood depth affected the survival of black willow. However, eastern cottonwood was threatened by flood depth, flood duration, and cumulative flooding temperature calculated by summing air temperatures while trees were flooded in 2019, 2020, and 2021. During the growing season, the models predicted that black willow could tolerate flood depth of 1.38 m in April, 1.52 m in May, and 0.74 m in June, while eastern cottonwood could tolerate 1.18 m in April, 0.86 m in May, and 0.85 m in June. Due to having higher flood tolerance thresholds, black willow had better survival and biomass production than eastern cottonwood. This study also identified critical physiological parameters that affected the biomass productivity of eastern cottonwood, black willow, and American sycamore (Platanus occidentalis). Results showed that the growth of black willow was driven by nitrogen per unit leaf area (R2 = 0.41 and P-value = 0.004) and photosynthetic nitrogen use efficiency (R2 = 0.27 and P-value = 0.03); American sycamore was determined by stomatal conductance (R2 = 0.68 and P-value = 0.04) and transpiration rate (R2 = 0.70 and P-value = 0.04); and eastern cottonwood was not affected by either water or nitrogen factors. Understanding physiological strategies of these species provides useful information when matching site-species for riparian restoration in the LMAV. This study also found that a SRWC plantation could mitigate agricultural runoff by removing 78 to 83% of nitrate-nitrogen and 70 to 73% of orthophosphate-phosphorus from the groundwater before discharge to the Yazoo River. Therefore, rather than abandoning these areas, establishing SRWC plantations for bioenergy on marginal cropland can mitigate agricultural nutrient runoff and improve the water quality of the LMAV.