this is not uncommon
in order to gravity drain and maintain minimum cover over pipes, the outfalls often end up submerged.  

your design may want to consider the tailwater level to be something higher than mean low water.  How about mean high water plus a storm surge?

Ok.  It is not uncommon to have a submerged outfall.  This is a 42" RCP about 5' below MLW.  The inlets and manholes area above that.  However, we do get some ponding around the closest inlets.  Maintenance says it is clear.  My understanding of hydraulics is that the 2-3' of head between the manhole water elevation and the MLW should be sufficient to drive the water through the pipe.  This isn't a situation with a large reservoir with 2-3' of head.  Only the small amount in the manhole and inlet.

you only need enough head to overcome the friction loss in the pipe and any other minor losses

Is the standing water a maintenance, nuisance or property damage issue?  While a common practice, I've seen where not venting the MH upstream of the submergence caused upheaval of its frame & grate during peak flow.  Or perhaps there's a transitory backwater effect due to moving the plug of water through the submerged pipe.

That's an interesting theory staffgage!  I suppose it is possible to get some air in the pipe.  The maintenance crew is going to try to bulkhead the outfall (with a diver) and then clean and TV the line to see if there are any obstructions.  The standing water is in a very visible commerercial area.

 In our local tidal areas, we have frequently had a problem with some inlets flooding due to unusually high tides or storm surge.  (This can really be a problem if it's salt water and asphalt pavement!) We have found some success with the installation of tide flaps at the outfall or at a large junction inlet just before the outfall. Just need to make sure that your system has enough head to ensure positive flow during a storm event, although the newer flaps don't need very much.

Good Luck

lsp_pe

In reply to the posts, my comments for what they are worth include:

flap gates are good is they can be maintained. it is more common for them to be forgotten and then get leaks rendering them pretty much useless. if they are in a location where it is difficult and costly to access there could be issues in the future.

secondly submerged outfalls are sometimes useful to disperse the fresh water from the cathment into the salt water of the harbour. it can look shocking in the harbour if there is a plume of fresh water (usually with suspended sediment) shooting out across the harbour.