Metolachlor (MET) is a widely used herbicide that can adversely affect phytoplanktonic non-target organisms, such as cyanobacteria. Chytrids are zoosporic fungi ubiquitous in aquatic environments that parasitize cyanobacteria and can keep their proliferation in check. However, the influence of organic pollutants on the interaction between species, including parasitism, and the associated ecological processes remain poorly understood. Using the host-parasite system consisting of the toxigenic cyanobacterium Planktothrix agardhii and its chytrid parasite Rhizophydium megarrhizum, we investigated the effects of environmentally relevant concentrations of MET on host-parasite interactions under i) continuous exposure of chytrids and cyanobacteria, and ii) pre-exposure of chytrids. During a continuous exposure, the infection prevalence and intensity were not affected, but chytrid reproductive structures were smaller at the highest tested MET concentration. In the parasite's absence, MET promoted cyanobacteria growth possibly due to a hormesis effect. In the pre-exposure assay, MET caused multi- and transgenerational detrimental effects on parasite fitness. Chytrids pre-exposed to MET showed reduced infectivity, intensity, and prevalence of the infection, and their sporangia size was reduced. Thus, pre-exposure of the parasite to MET resulted in a delayed decline of the cyanobacterial cultures upon infection. After several parasite generations without MET exposure, the parasite recovered its initial fitness, indicating that detrimental effects are transient. This study demonstrates that widely used herbicides, such as MET, could favor cyanobacterial bloom formation both directly, by promoting cyanobacteria growth, and indirectly, by inhibiting their chytrid parasites, which are known to play a key role as top-down regulators of cyanobacteria. In addition, we evidence the relevance of addressing multi-organism systems, such as host-parasite interactions, in toxicity assays. This approach offers a more comprehensive understanding of the effects of pollutants on aquatic ecosystems.