I would like to update my model which is currently providing current day flows to natural flows. As I remove my demand nodes, the flow increases overall but also reduces in some areas. I would be interested to know which inputs are often updated to bring about meaningful results.

Anabel,

Do you have return links in your model? I suspect any of the flow decreasing may be due to return flows.

In general, to model natural flow, my practice is to inactivate demands as you say, plus inactivate reservoirs (you can set them to inactive in certain scenarios, or just set storage capacity to 0), flow requirements, and any man-made diversions.

How detailed you should go will depend on the goals of your model and your definition of "natural flows". Is your goal to model the hydrology of the existing land use but absent any major human operations? Or is your goal to model the hydrology of the land use in absence of any human development? Depending on your answer to this, you may consider changing the land use class of any developed land cover classes (urban, farming, etc). But, certainly not every model does this.

Cheers,
Doug