The longitudinal profile you have sent shows a not uncommon annoyance of the current, and previous, HEC RAS.
The profile appears to pick out the lowest level on a given bridge deck, which in your case has been computationally laterally extended to include the upstream and downstream cross sections (ground level/high chord - see leftmost point on cross section below).
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Whilst this is sometimes useful, (showing when a bridge is bypassed or overtopped at its lowest deck/parapet level) it is also misleading in other circumstances, and can look most odd when presenting the results. Your long section (shown above) does look like the bridge is being overtopped, when in fact, the deck/parapet level is some 400mm above the lowest plotted 'deck level', and the lowest plotted 'deck level' 200mm below the channel levee marker.
I have heard, somewhere, an official explanation for this phenomena, but as yet have not found a fix for it! It should be relatively simple to code, possible offering an option for plotting of the lowest section level (as at present) or of only the bridge high chord?
Where I have needed to present the results without this distraction, I have either manually added the true bridge levels by pen, or adjusted the upstream and downstream bridge cross sections. In you case, the water level at the Q50 does not come out-of-bank. Therefore, you could replicate the sections (e.g. 0.53 and 0.49) as dummy sections, and delete the low ground on the left bank. The results are shown below.
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I hope this helps slightly?
Regards
Mike Vaughan BEng CEng MICE
VaughanM@pbworld.com