The paper considers methods and information technologies for full automatization of forest ecosystems sustainability estimation. Analysis of forest ecosystem sustainability is explored as a multi-objective problem with applying a complex of models for calculating partial indicators of sustainability. Earth observation (EO) data is used as an essential component of information support for estimating forest ecosystems sustainability indicators. Methodological framework of automatization consists of complex modelling, application of models qualimetry methods for selecting specific calculation models, and methods for multi-criteria analysis to estimate generalized indicators of sustainability. A software architecture is proposed in order to implement procedures of complex modelling with integrated processing EO and field data.