Raj --
My understanding is that QUAL2E requires some amount of chlorophyll a in the stream to start with, or else its calculations somehow fail. So SWAT always adds some "starting" chlorophyll a to each stream reach, in case QUAL2E is turned on.
If QUAL2E is turned off, this chlorophyll just passes downstream without impacting nutrient loads.
However, if QUAL2E is turned on, then it interprets this chlorophyll as algae. When that algae decomposes it further presumes that the nutrients in that algae are released to the stream, according to the P and N content parameters (the fraction of algal biomass that is P and N -- you can set this). The problem is, this is all "extra" P and N that are not related to the actual loads of P and N transported by the overland runoff (or any other flow) in SWAT. I.e., this extra P and N are not "real."
Depending on your watershed, the added amount may be significant. In my last project, turning on QUAL2E resulted in a 20% increase of the P load. I felt this was unacceptable, and since then I just haven't used QUAL2E at all.
The error can be reduced by reducing the P and N content of algae to negligible levels (like, from 0.015 to 0.001 or something like that, if I remember the values more or less for P). However, then your QUAL2E calculations of algal growth and decay per unit nutrient level will be pretty screwed up.
That's the current state as I see it now; the code has not been corrected to my knowledge. The fix would be to simply check to see if QUAL2E is turned on, and if it is, then the portion of the P load from the HRU corresponding to the amount of added algae (chlorophyll) should be subtracted from the other P-load components (ORG_P, SED_P, and SOL_P) before being delivered to the reach. Reducing the size of the "seed" load of chlorophyll might also be appropriate.
Cheers,
-- Jim