Most of the agriculture in the Great Plains and western U.S. is water-limited, consisting of rain-fed, dry-land, cropping systems or range-livestock systems and some irrigated cropping systems where irrigation water is available. Prolonged drought in the last few years has aggravated the situation, and greater frequency of severe droughts predicted by global climate change models is a cause for great concern, especially for dry-land systems. At the same time, the increasing water demands for drinking, sanitation, urban irrigation, industry, and environmental uses are outbidding and reducing the irrigation water available for agriculture. Similar situation exists in many other arid to semi-arid parts of the world. To obtain maximum return out of limited rainfall and irrigation water, with minimum environmental impact, the producers need whole-system and quantitative management tools to help them optimize the use of available water and minimize associated inputs on site-specific and field-specific basis. The tools should help determine appropriate crop sequences, and optimize the use of limited rainfall and irrigation water with respect to the amounts and timings of rainfall, critical growth stages of crop, soil fertility, and weather conditions; help determine an optimal selection of alternate crops during droughts; and an optimal allocation of limited water among crops. There is currently great excitement about growing bio-energy crops in the area, including the dry-land oil seed crops and irrigated corn or other biomass crops. The above tools should also be able to evaluate the long-term economics of bio-energy crops while leaving enough crop residues on the soil to maintain soil organic matter.