In DELWAQ discharges are exclusively sources of mass. The actual
water volume associated with a discharge has to be in the hydrodynamic
model. In that respect the flow rate as you specify it in the input
for DELWAQ is merely a convenience: you can then specify the flow rate
and the concentration instead of the mass per second.
There is more to it, as you can also specify extractions and other
variations, but for that I refer to the manual.
Not all discharges that are of interest to water quality may be
incorporated in the hydrodynamic model - say you have a discharge that
is not going to influence the flow field in any way, but is quite
polluted, such as the discharge of untreated wastewater. That sort of
discharges can be defined independently of the hydrodynamics.
If the discharge is defined in the hydrodynamic model, it is probably
best to accept the discharge rate from that calculation and simply add
information on the concentrations for the various substances.