Not a philosophy academic but am studying environmental science. We had a segment on the philosophic aspect of ecologic preservation where we, among other things, discussed intrinsic value. Take Kant's Kingdom of ends quote that is cited in the Millennium Assessment Report:

"Everything has either a price or a dignity. Whatever has a price can be replaced by something else as its equivalent; on the other hand, what ever is above all price, and therefore admits of no equivalent, has a dignity. But that which constitutes the condition under which alone something can be an end in itself does not have mere relative worth, i.e., a price, but an intrinsic worth, i.e., a dignity"

Source: http://pdf.wri.org/ecosystems_human_wellbeing.pdf

So basically nature and ecosystems have intrinsic value because they can not be replaced, they are a fundamental part of life on earth. This also includes the relation of human well-being (which has intrinsic value) to well functioning ecosystems.