Water hyacinth (Eichhornia crassipes) is native to the Amazon basin and is one of the worst aquatic weeds in the world. It has been an invasive species in aquatic ecosystems of northern Iran since 2011. The use of herbicides as a method of plant control is common and efforts are made to select a formulation with the least impact on the environment. In the current study, three types of herbicide including glyphosate (Roundup), Glufosinate-ammonium (Basta) and Bispyribac sodium (Nominee) were used to control water hyacinth and the effects of their use on the abundance and diversity of planktonic communities were investigated. Roundup treatment has an immediate effect on water hyacinth, while Basta and Nominee treatments were effective for a longer period of time. Results showed that about 90% of phytoplankton and 71% of zooplankton belonged to the diatom and protozoa, respectively. The diversity of plankton species did not change after herbicides application and the number of genera in control ponds was almost constant. The phytoplankton abundance was higher after herbicides applications, especially in the Roundup treatment. The used doses of herbicides not only had a controlling effect on water hyacinth but also had no significant negative effect on the diversity and abundance of planktonic communities.