While modern weedkillers are great about using fewer chemicals and therefore less runoff into streams, the organic manufacturing process uses older, less effective compounds and that means on a calorie-per-calorie basis, the harm to the environment may be substantial. Water contaminated with copper sulfate, the most popular organic weedkiller, is harmful to crops, animals, and people.

It's a $130-billion-a-year industry, so efforts are on to recycle more harmful chemicals used in the organic process, and that can help conventional farming also. For example, a new effort uses pyrolis - heating without oxyen - of biomass like plants, trees, or animal waste to create biochar. The kicker is that the biochar will be supplemented by phosphorous, making it good plant food, extracted from wastewater, making it a win for the environment.(1) 

Phosphorous is a key ingredient in fertilizer and, unlike modern pesticides like neonics, it can't be efficiently targeted. It has to be extracted and then processed. In 20th century farming like the organic segment, a lot is used, which means a lot can run into water. Biochar is basically charcoal, which makes it a good filter, and also a sponge for runoff like nitrogen and phosphorous. 

Sorption isotherms of phosphorus on unmodified and modified biochar. Solid lines are fits of isotherms using either the Langmuir (AD) or Freundlich (BN and AC biochar) models. https://doi.org/10.1371/journal.pwat.0000092.g001

The new work experimented with extracting phosphorous from municipal wastewater to create a slow-release fertilizer. It's still in the early experimental stage, they have to supplement with iron to get it to work optimally and that will be a non-starter because environmental lawyers will sue any company doing that out of existence.

But it is an intriguing waypoint on the road to better recycling of agricultural inputs to make better inputs.

NOTE:

(1)
Even the NYU School of Journalism can't find a way to make that science sound evil for their friends in the organic industry.

Sorry, "Arthur L. Carter Journalism Institute." I will get their name right when their Dean creates a social media policy that doesn't allow their fat-cat teachers, grossly overpaid thanks to exploitative student loan debt, to stop libeling people.