...or did you mean that we tap the end of the discharge pipe for a controlled farm? Flying by the seat of my pants here, that sounds like a tempting idea. Open systems, such as wild blooms in the ocean, can be a real problem, but if the discharge was incorporated into a marine farm having a closed system, in broad strokes here, that could work.
As a best case, I would think, treatment on the front end would likely need to be significantly modifed, but waste products tend to be great sources of nitrogen and phosphorous - which is also critical to growth. The big problem that I do see here is that of toxins, industrial chemicals, and even measurable levels of drugs, like morphine! As it stands now, raw sewage is a real witch's brew. I don't know what the potential for serious drawbacks may be if algae intended for fuel is used to treat an uncontrolled discharge. For that reason, I would expect it likely that front-end treatment would be critical, with mainly the nitrogen and phosphorous left for the algae, at the discharge pipe.