Does the network you're working in have more USGS flow meters than just the three that overlap with your sampling stations? If so, you should be able to interpolate a flow regime for most of the network. It wouldn't be at a level of accuracy that I'd like to see for a thesis though.
With only three flow guages assuming that they're on the mainstem of your watershed, you should be able to build a model for the mainstem alone to build a function to relate the flow accumulation to those sample points and at least have a statistically derived regression (with the all important R^2 values though they'll be large). The more flow guages you have the better as far as the regression goes.
The flood event time series is going to be a real challenge though. You may or may not need to take that into account. You know what your region and needs are and will have to make that call. If you do need it, it will take a lot of work (second thesis?).
I've done a fair amount of GIS modeling on streams for TMDL purposes, so drop me a line <username>@hotmail.com
"if the city is visibly one of humankind's greatest achievements, its uncontrolled evolution also can lead to desecration of both nature and the human spirit."
-- Melvin G. Marcus 1979
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