Environment Agency policy adviser Jo Kennedy said that under the directive, EU member states must aim to achieve "good status" in water bodies by 2015.
Environmental quality standards (EQS), which set limits on the concentration of specific substances in water, form part of that.
Although glyphosate has not been subject to an EQS in the past, Kennedy said it is a candidate for regulation in the future, along with carbendazim and chlorothalonil.
Kennedy said: "Diuron has been one of the top pesticides in terms of contamination in rivers. But the compliancy issue has been solved by the removal of diuron products from the market. There will be extra scrutiny on glyphosate."
She added that the danger was, with diuron excluded from the market, the use of glyphosate would increase, potentially leading to higher concentrations in water. "The amenity sector needs to be ahead of the game on glyphosate."