Don't know about a specific model you could insert the numbers into (although I guess you could use the BMWP using the macroinvertebrates present to assess water quality), however not for nitrogen and phosphorous. Experimentally, you could do an algal bioassay to see which is the limiting nutrient bearing in mind the Redfield Ratio (106:16:1 for C:N:P). Always useful to do anyway - but if you do make sure that you remove the zooplankton/macroinvertebrates from your water sample otherwise you'll have nothing to measure. This method will show you the limiting nutrients and the levels of algal growth. 

 There is also the Biological Oxygen Demand that could be a useful indicator of microbial activity

I'm not sure if I understand your question well. I've attached a few links to reviews or reports about models for specific water bodies in Oregon, USA. Hope this helps..

http://www.usbr.gov/mp/kbao/waterquality/klamath_river_model_review_final.pdf

http://or.water.usgs.gov/pubs_dir/WRIR01-4041/

http://www.deq.state.or.us/wq/tmdls/docs/klamathbasin/ukldrainage/tmdlwqmp.pdf

SWAT (Soil and Water Assessment Tool) is an open domain (free) water quality modeling software you can download from the internet.  It's been used in watersheds all over the world, so you might be able to find journal articles using SWAT in Peru or another similar watershed to your study.  You can run SWAT with geospatial data in ESRI ArcGIS and also as a stand-alone model without mapping software.  You can use your own P and N data for model calibration and validation.  Check out the SWAT webpage:  http://swat.tamu.edu/      The developers are also very helpful if you have any questions, and they have lots of documentation and workshops.

WARMF (Google it) is another river basin model that can be used. It is an integrated model of land catchments, river segments and lakes. It calculates nonpoint source loads of P and N from tributary land. It accepts point source discharges of P and N to river segments and lakes. It simulates such water quality parameters as temperatures (stratification and destratification of lake), dissolved oxygen, total suspended sediments, algae (diatom, green and bluegreen). It can calculate the total maximum daily load (TMDL) of P and N to prevent the chlorophyll from exceeding a specified level.

the following link may be useful for you;

http://link.springer.com/article/10.1007/s11270-009-0056-2

http://link.springer.com/article/10.1007/s11269-009-9421-6

http://link.springer.com/article/10.1007/s10661-009-1142-z

QUAL2K (or Q2K) is a river and stream water quality model

http://epa.gov/athens/wwqtsc/html/qual2k.html

QUAL2K Model Information

Key Words

aquatic biology, assessment, compliance, discharge, environmental effects, hydrology, NPS related, NPDES, point source(s), surface water, test/analysis, TMDL related

Pollutant Types

Conventional Pollutants (Nitrogen, Phosphorus, Dissolved Oxygen, BOD, Sediment Oxygen Demand, Algae), pH, Periphyton, Pathogens

You could consider BATHTUB. It is a simplified model for assessing eutrophication in Lakes: 

http://wwwalker.net/bathtub/help/bathtubWebMain.html

It was developed by Dr. William W. Walker, and has a moderately large user base including the US Army Corps of Engineers. There are many applications of this model, and I attach the publication by Dr. Kyle R. Douglas-Mankin because he is a colleague.

http://wwwalker.net/bathtub/help/bathtubWebMain.html

Article Watershed-lake water quality modeling: Verification and application

I'm doing same study for simulating phosphorus  and SWAT it does do that . I've a question about INCA-P software(integrated Catchment for phosphorus model ) . Does any body know about this software and from where can I get it ?