This paper applies a social metabolism framework and energy flow analysis for evaluating agroecosystem and land use transitions in food-energy-water systems using the Upper Snake River Basin (USBR), Idaho, USA as a case-study. The study area is one of the primary agricultural regions of the State of Idaho. Dairy products are the primary agricultural outputs of the region; therefore, we modified a biomass accounting framework to explicitly incorporate the role of manure in the agroecosystem. Despite the increase of cropland between 2002 and 2012 in the basin, a decrease in energy input was observed for crop production. An increase in the industrial energy inputs for dairy production, on the other hand, showed that the basin is a clear example of a metabolic industrialized farm system - an example of land use intensification. We compare the energy return on investments (EROIs) as an indicator of agroecosystem transition for both crop and dairy production during the period 2002 to 2012. Contrary to our expectations, the analysis suggests that livestock production is a relatively energy efficient process in land management in the basin. This is due to the reuse of nutrient by-products from livestock as well as the refuse and residues from crop farming. At the same time, the findings provide insights on the percentage of manure to be reinvested as compost that would improve energy production efficiency. However, the reuse of manure, as it is managed in the basin, may have a negative implication on the nutrient balance of the agroecosystem that needs further investigation. Nonetheless, there is market potential for the reuse and reinvestment of biomass to make energy production in the basin more efficient.