Farm-level trade-offs between development objectives are analysed using a three-stage methodological design. Firstly, a typology of arming systems is devised, using data from a farm-level survey and the methods of principal components analysis and cluster analysis. Five farm types are described that characterize current production practices in two regions in the Philippines. Secondly, a set of sustainability indicators are measured for each of the five farm types. Finally, the sustainability indicator results are analysed in a participatory multi-criteria decision-making model using weights established during a series of focus groups with stakeholders in the study regions. Very large farms perform particularly badly in these analyses, and the optimal farming system varies across social groups. The implications for the management of the sector are discussed, particularly in relation to aquaculture’s continued exemption from agrarian reform legislation.