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...the Winooski's Montpelier gauge is upstream of the Mad River confluence. The gauge downstream of the Mad is in Essex.
See the USGS streamflow gauge index page for VT/NH. On the individual gauge pages, note the "Available data for this site" drop-down menu near the top of the page. It includes a 'Location map' option. For example, that can help you determine if the Montpelier gauge's flow includes flow from the Dog River, which comes into the Winooski on the west side of Montpelier.