The development of shrub willow as a bioenergy feedstock contributes to renewable energy portfolios in many countries with temperate climates and marginal croplands. As willow is developed commercially in the US Northeast, there is a need to better understand its impact on water quality and greenhouse gas (GHG) emissions compared to alternative land uses (e.g., corn, hay). We measured the impact of cultivated willow of various ages (2 and 5 years) and management strategies (fertilized vs. unfertilized) compared to corn and hay on water table depth, soil water NO3- and PO43- concentrations, and (NO)-O-2, CH4, and CO2 fluxes at the soil-atmosphere interface during a drier than normal year in heavy clay soils with marginal agricultural value in upstate New York, USA. Soil water concentrations resulted in higher PO43- in willow and higher NO3- in corn and hay, although willow is unlikely to negatively impact water quality with respect to phosphorus due to shorter periods of hydrologic connectivity in willow and hay than in corn. Gas fluxes varied spatially and temporally with hot moments of CH4 and N2O in corn and hay and seasonally variable CO2 in willow. While CH4 did not vary between fields, N2O was higher in corn and hay, and CO2 in willow, resulting in no net difference between CO2 equivalent (CH4, CO2, and N2O) emissions between fields. Converting marginal cropland on clay soils from corn or hay to willow left overall GHG emissions unaffected, slightly increased PO43-, and decreased NO3- concentrations in soil water.