Farmers have been increasingly called upon to respond to an ongoing redefinition in consumers' demands, having as a converging theme the search for sustainable production practices. In order to satisfy this objective, instruments for the environmental management of agricultural activities have been sought out. Environmental impact assessment methods are appropriate tools to address the choice of technologies and management practices to minimize negative effects of agricultural development, while maximizing productive efficiency, sound usage of natural resources, conservation of ecological assets and equitable access to wealth generation means. The 'system for weighted environmental impact assessment of rural activities' (APOIA-NovoRural) presented in this paper is organized to provide integrated farm sustainability assessment according to quantitative environmental standards and defined socio-economic benchmarks. The system integrates sixty-two objective indicators in five sustainability dimensions (i) Landscape ecology, (ii) Environmental quality (atmosphere, water and soil), (iii) Sociocultural values, (iv) Economic values, and (v) Management and administration. Impact indices are expressed in three integration levels: (i) specific indicators, that offer a diagnostic and managerial tool for farmers and rural administrators, by pointing out particular attributes of the rural activities that may be failing to comply with defined environmental performance objectives; (ii) integrated sustainability dimensions, that show decision-makers the major contributions of the rural activities toward local sustainable development, facilitating the definition of control actions and promotion measures; and (iii) aggregated sustainability index, that can be considered a yardstick for eco-certification purposes. Nine fully documented case studies carried out with the APOIA-NovoRural system, focusing on different scales, diverse rural activities/farming systems, and contrasting spatial/territorial contexts, attest to the malleability of the method and its applicability as an integrated farm environmental management tool.