The capabilities approach has attracted broad interest in environmental ethics. One very interesting application is the environmental or extended capabilities approach which promotes the notion of environmental capabilities that contribute to the flourishing of non-human beings and ecological systems. The approach however lacks any account of the capabilities of ecological systems. This essay applies the environmental capabilities approach at the ecosystem level and examines how the flourishing of an ecosystem can be understood in terms of capabilities. Ecosystem flourishing presumes the ability of a given system to maintain its characteristic functions, diversity and quality, and do so even in the face of various disturbances. Resilience can be understood as a central capability of ecosystems to maintain their characteristic functioning in disruptive circumstances, which is particularly important with regard to human-induced environmental changes. This argument evokes duties of ecological justice regarding ecosystems. The nature of these duties is considered and linked with a discussion on how the environmental capabilities approach can promote more holistic decision-making.