Nikolay -
I haven't seen a response to your question, so I'll try from memory. The three forms of phosphorus delivered from the land (HRUs and subbasins) are, basically, (1) soluble P, (2) particulate mineral P, and (3) particulate organic P -- here I'll call them sol_P, min_P, and org_P. The particulate forms include (I think) both "active" (= easily desorbed) and "stable" forms of P. In addition, groundwater can deliver P to the channel -- I'll call that gw_P.
When these 3 forms of phosphorus are delivered to the reach, they are converted into the two categories (which is what I presume Qual-2e requires) called mineral and organic P. Here I'll call them reach_min_P and reach_org_P. The output from the subbasin (sol_P + min_P + org_P + gw_P) equals the input to the reach (reach_min_P + reach_org_P). This conversion is confusing -- but I believe it's close to the following:
reach_min_P = sol_P + gw_P + active_min_P + active_org_P
reach_org_P = stable_min_P + stable_org_P
(You really should double-check that this is what the code is doing -- I'm operating from memory.)
This conversion results in the convention that reach_min_P fraction essentially equals the dissolved P content in the reach, and the reach_org_P fraction essentially equals the particulate P content in the reach (including P adsorbed to mineral particles). I've always been somewhat uncomfortable with a model such as Qual-2e that doesn't explicitly include a mineral-adsorbed particulate P fraction, since this fraction is commonly large in rivers in agricultural regions.
In addition to other landscape sources of P, the subbasin adds chlorophyll to its reach. If you don't turn on Qual-2e, this chlorophyll remains simply as chlorophyll and doesn't impact the P budget of your model. If you turn on Qual-2e, it commonly assumes this chlorophyll is from algae, and when it decomposes this presumed algae, it adds extra phosphorus to the reach, based on the assumed P content of algae. This is all in addition to the sol_P, min_P, org_P, and gw_P delivered from the subbasin to the reach.
Cheers,
-- Jim