Habitat assessment essentially seeks to answer the question of how capable is an area in terms of supporting native ecosystems. For a river, there is the aquatic ecosystem assessment and riparian corridor assessment. Aquatic assessment is often based on biotic indices of water quality and watershed health based on aquatic macroinvertebrates ( that requires some prior baseline data on what species and communities are found there, but one can always begin this study). In addition, a rapid assessment also notes the channel morphology - of the pools, riffles and channel bank stability conditions. For instance, deforestation or land use change in the upstream watershed can lead to sedimentation of the stream bottom, thereby removing habitat for macrioinvertebrate larvae, and thereby affecting prey for fish and amphibians, with cascading effects up the food web. As streamflow data is rarely available, one uses biotic indices - if sensitive organisms are present, that indicates flows are still following a seasonal pattern that existed for long.

Then comes the assessment of the vegetation on the shore - species composition, whether there are any signs of shore mass wasting and soil erosion.

For forests, usually a species composition and abundance survey can be done using some kind of transects ( line or plot), and compared to any old survey data ( if available ) or local knowledge of what trees have been in that forest/area for the past couple centuries. Certain trees or old fallen logs are also specific habitat for some wildlife. Presence of invasive exotic plants could also be noted, as is the general soil ( whether bare or litter-covered) and understorey.

There is a lot of info online - and they share a generally similar approach. The basic objective is to assess how pristine or degraded a region has become, to support the diversity of life that existed there recently. The challenge in most places is a lack of documented data of what plants and animals existed there recently. As you mention the area is large, perhaps one can access Google Earth to examine the canopy of the forest, combined with some ground truthing to assess whether the canopy is intact or degraded/secondary forest.