In order to assess the ecological sustainability of agricultural production systems, there is a need for effective tools. We describe an environmental systems analysis tool called SALSA (Systems Analysis for Sustainable Agriculture). It consists of substance/material flow models in which the simulation results are interpreted with life-cycle assessment methodology. The application of SALSA is demonstrated in a case study in which three different ways of producing pigs are compared with respect to energy input and the environmental impacts of global warming, eutrophication, and acidification. The scenario that combined a low-protein diet without soy meal with an improved manure-management technique with low nitrogen losses was the best for all impact categories studied. The strength of the SALSA models was their capacity to capture consequences of management options that had an influence on several processes on a farm, which enabled the type of complex studies we describe.