The study shows the water footprint of sugarcane and cassava production in northern Thailand for the period 2008-2010. It has shown volume of freshwater use per average yield. The result showed that the average WF of cassava is 2.5 times more than that of sugarcane. The differences in the value of WF are caused by various factors, including climate, crop characteristics, agricultural production system which differs for each region. For example, Kamphaeng Phet has the smallest WF for both sugarcane and cassava where yield of sugarcane is lower than in Nakhon Sawan and the largest of cassava in northern Thailand. The result shows the WF are somewhat similar for each province. For example, the WF of sugarcane from Kamphaeng Phet is 1.5 times larger than that form Lampang. The WF of cassava from Uthai Thani is 1.2 times larger than from Kamphaeng Phet. At the present, the northern region has witnessed an increasing trend for cultivation area and production yield. The demand for bioenergy in Thailand has increased too. The bioenegy derived from biomass uses freshwater for agricultural production system. If the demand of biomass increases the volume of water usage also increases. The results from this paper can be used to prepare suitable guidelines for the management of water resource and increase crop yield. As bioenergy is promoted to decrease the impact of fossil fuel on climate change, it will also bring non-sustainable water resource and raise confliction between “water for food” and “water for energy” [4].