Arundo donax (Giant Reed) is quickly being developed as a rapidly-growing, robust, and highly productive bioenergy crop, with large scale cultivation of this species planned for the Columbia River basin of the Pacific Northwest (USA). Despite its potential as a next generation biomass crop, relatively few studies have examined the physiological performance of A. donax under agricultural conditions. Unlike traditional crops, A. donax is known to be a high-emitter of the volatile compound isoprene, which may significantly impact regional air quality, but it has not been widely cultivated in North America and little is known about how this species will perform in the Pacific Northwest. Over two field seasons, we measured isoprene fluxes from A. donax plants in both greenhouse conditions and in an agricultural field setting under a variety of conditions and fertilizer treatments. We also measured several other attributes of A. donax productivity and leaf physiology including chlorophyll content, photosynthesis rate, stomatal conductance, specific leaf mass, water use efficiency and gas exchange. We found that A. donax physiologically performs well under cultivation in the Columbia River basin, but that it also emits isoprene at significantly higher rates than previous reports indicate. We also found that both isoprene emission and leaf physiology were highly affected by agricultural management decisions, including nitrogen and irrigation management. Our findings indicate that crop management strategies can be developed that simultaneously seek to minimize isoprene emission while maximizing biomass production in this newly emerging bioenergy crop.