It depends on where the infrastructure is, often times farmers end up removing trees or vegetation as they want to maximize their yield and see this as an intrusion that could activate environmental reg. Though personally, I do see the longterm benefits of working with the environment by planting trees, buffer strips etc.
Another approach, that is a bit more upstream, is precision agriculture - i.e. reducing the amount of N and P applied in the first place.
Possible green projects for additional treatment and use of wastewater containing nitrogen and phosphorus, using a environmentally friendly and safe minerall sorbent. having adsorptive, reducing, bactericidal and other properties. Projects are most effective for small towns, urban and rural settlements.
It depends which runoff areyou talking about. Since you refer to N and P, I suppose you are talking about agriculture runoff, and you would like to avoid nutrient discharge in water bodies to limit the risk of eutrophication. If this is your case, I suggest you filter strips along the river to treat the runoff before it enter in the river, or constructed wetlands for agricultural runoff treatment
The question may not be only about agricultural runoff. Sewage overflow and septic tank seepage can contribute N and P. But I agree with the filter strip and constructed wetland recommendations, and also with Richard Ashley to consider SUDS (see also WSUD) solutions.