In this work, emergy analysis was used in association with the Geographical Information System (GIS) in order to improve the evaluation of family-managed farms that adopt either the ecological or the chemical production models. Three small farms, located in Amparo County, in São Paulo state, Brazil, were studied. One of them, Duas Cachoeiras farm, uses agroecological concepts for its agricultural production. The two others (Santa Helena farm and Três Lagos farm) use the conventional chemical model. In an attempt to improve the precision of the data used in emergy analysis, the Universal Soil Loss Equation (USLE) was incorporated to the GIS tool to calculate the topsoil loss in the farms. The GIS tool also allowed the calculation of the amount of rain water that infiltrates the ground and can recharge the aquifer. This percolated water is a system output and was incorporated in the emergy accounting. Another modification in comparison to previous emergy analyses was that the renewability factor of each input was considered in the emergy accounting. Results showed that the agroecological farm is more sustainable and can be used as a model for small farms in their transition to ecological agriculture. The GIS-emergy tools were used to compare the environmental performance of the four main productive areas of Duas Cachoeiras farm (annual cultures, orchard, forest, and pasture). These results demonstrate the emergy performance of each kind of land use and may be used in watershed planning. © 2007 Elsevier B.V. All rights reserved.