Wait, back up.
Your existing site has a 100 year retention pond with no outlet control device that caught and held the full 100 year runoff from 3.9 acres of development, even though it was adjacent to a stream?
So your existing site has zero discharge?
A) Are you sure about that?
B) Where is this project at?
C) How does the existing pond draw down to empty? Groundwater infiltration only?
C2) If so, why connect it to the stream at all? Isn't it currently groundwater fed to the stream elevation via water table connectivity?
In most areas I've worked in, your post development discharge can't exceed your predevelopment discharge, which in your case is .. zero?
Do you have some maps or something?
All that aside, I would use SWMM (EPA-SWMM or XP-SWMM) to model what you've got going on. You can do a stream flow model for the overall watershed, complete with HEC-RAS style cross sections, put your current watershed and pond online, and watch the tailwater spill into your pond when you route the storms. I would NOT use Hydraflow, and I'd have an honest heart to heart with Peter Smart before using HydroCAD, although HydroCAD might handle it if you made some very bland assumptions about the geometry in your stream channel. If I was stuck using Hydraflow, I'd do what Francesca suggested, and route a hydrograph through HEC-RAS to get a variable tailwater to work with, presuming Hydraflow can even handle that, which I'm not sure it can. I haven't used it in years.
Hydrology, Drainage Analysis, Flood Studies, and Complex Stormwater Litigation for Atlanta and the South East -