I cannot advise on SWMM. But a flooded urban area is going to have much different water quality from river in most instances. Stormwater and sewer pipes, septic systems, gas storage tanks, pet and animal wastes, fertilizers, pesticides, failed or overwhelmed waste storage ponds, etc. can add to water quality issues in flooded urban areas.

You cannot assume flood water quality in the 2D domain is exactly equal to main channel, it has to be modeled on its own.

I worked with XPSWMM and XPFlood (basically same solver in different GUI) if your transport solver (means water quality solver) works, it works everywhere, there most be something in the setting or parameters wrong or problematic that you do not get the water quality okay. My suggestion:

Set up a very simple problem , river with 4 cros-section (only one reach) and a levee and a 2D domain next to that, send a simple hydro-graph inside with water quality on and see if it works in the simple problem or not (very small river attached to very small 2D domain, simple slopes, simple roughness, ...) First get this right and if you cannot send that to the software developers. It is almost impossible to debug and narrow down to your problem in a very large problem which has lots of complexity.

Thanks a lot for all of your recommendation.

Good Luck

TELEMAC-2D , PCSWMM (2D)