Technical Abstract: Dairy and beef farms are major contributors to the economy of the northeast region. Increasing production costs, static or declining product prices, and environmental issues though, are jeopardizing the long-term sustainability of these farms. More efficient, economical, and environmentally sound production practices are needed. Integrated crop, pasture, and livestock farms form complex physical and biological systems. Only by studying the farm as a whole can improved practices be developed that maintain a reliable food supply, a strong agricultural economy, and a safer environment. Our goal is to develop and apply software tools for comprehensive evaluation of the impacts and interactions of farm management on air and water quality while maintaining or improving farm profitability. Specific objectives are to 1) develop process-based relationships that predict emissions from animal, feed, and manure sources on dairy farms, 2) quantify carbon sequestration potential of temperate grasslands, and 3) validate and use farm and watershed scale models to assess the effects of conservation practices on farm management and our soil and water resources. The evaluation of alternative production systems provides information that helps direct and encourage producers, and those consulted by producers, toward management options that improve their farm's potential impact on the environment while maintaining or improving profitability.