Field evidence supports former experimental claims on the stimulatory effect of glyphosate on picocyanobacteria communities.

•We surveyed glyphosate-impacted (Pampean) vs -not impacted (Patagonian) lakes.•Herbicide impact indicators included: concentration, degradation genes and land use.•Picocyanobacteria (Pcy) abundance was higher in Pampean lakes.•Pcy abundance could be related to glyphosate indicators in the Pampa region.•Prolonged (>30 yrs) agricultural practices shaped freshwater microbial communities.