Changes in land use-land cover alter many environmental parameters, such as soil properties, water fluxes and availability. In agro-ecosystems (agricultural and bioenergy), the change in water exchange between land and atmosphere (evapotranspiration, ET) is key to net flow and availability of water on surface and below ground. In this study we examined changes in evapotranspiration due to land use change at two sites, one of which was corn-soybean cropland prior to conversion and the other 20yr in CRP brome grass. The study was conducted on the Great Lakes Bioenergy Research Center’s (GLBRC) Scale-Up sites in Southwest Michigan. Three sites were converted from agricultural (Corn-Soybean) to corn/ Switchgrass/ native prairie cropping systems, while other three were converted to same land use from grasslands under CRP (Conservation Reserve Program). Over a period of two years we monitored the water and energy fluxes on the converted sites (10-21 ha) using eddy-covariance systems installed near to center of each site. To describe the effect of land use change on the ET fluxes we examined the role of crop choices, soil and land quality, and agronomic management over a 2 year transition period to three bioenergy cropping systems: corn, switchgrass and native prairie. Comparisons were made to soybeans and Brome grass (CRP grass) which were included as transition crops. Based on total water losses during the study period, only conversion to corn (continuous) changed a landscape to water deficit for grassland to bioenergy scenarios; while conversion to corn (continuous) as well as Brome grass (CRP) changed a landscape to water deficit for cropland to bioenergy scenario. Our results indicated that crops as well as agronomy played an important role in determining annual water balance and availability of water in a landscape. Water availability in a landscape will be determined by the crops and agronomic practices followed. This could have large implications for water allocation and water availability to communities in the supported ecosystems.