Can a 'Habitat Risk Assessment' be used for assessing the freshwater river ecosystem?

Yes, it sure can! The risk assessment framework is agnostic to the type of ecosystem even though the documentation uses a marine/coastal system as an example.

I don’t have any references for you offhand, but you may download and explore a database of publications that have used InVEST models, and search by the HRA model. https://purl.stanford.edu/bb284rg5424

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