Written by Chris Goodell, P.E., D. WRE | WEST Consultants
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A limitation in HEC-RAS unsteady flow is that at junctions, RAS will project the downstream water surface elevation to the 2 upstream cross sections across the junction. Then the energy grade at each upstream cross section is back calculated. The result, especially if your cross sections are spaced far away from the junction is a depth that is too low at the upper cross sections, resulting in a large velocity head, and a huge jump in energy. To balance the energy from that cross section to the next one upstream results in a large increase in water surface elevation. This is a common experience at junctions in unsteady flow modeling and will look similar to this in a profile view. A tell tale sign of this problem is if you see the cross section on the upstream side of the junction go supercritical.

The way to fix this is to move your cross sections as close to the junction as possible (or add cross sections closer). This will minimize the negative affect of the junction limitation in RAS. Also, adding more cross sections between the cross section just upstream of the junction, and the next one upstream, will minimize any residual jump in water surface elevation while trying to balance the energy.