Abstract Worldwide, conventional agriculture makes extensive use of pesticides. Although the effects of herbicides are relatively well known in terms of environmental impacts on non-target organisms, there is very little scientific evidence regarding the impacts of herbicide residues on aquatic arthropods from tropical conservation areas. This study evaluates for the first time the toxicity of the herbicides ametryn, atrazine, and clomazone on the aquatic insect Limnocoris submontandoni (Hemiptera: Naucoridae). The lethal concentration (LC50) of herbicides was evaluated for these insects, as well as the effect of the herbicides on the insects’ tissues and testicles. The estimated LC50 was 1012.41, 192.42, and 46.09 mg/L for clomazone, atrazine, and ametryn, respectively. Spermatocyte and spermatid changes were observed under the effect of atrazine, and effects on spermatogenesis were observed for some concentrations of clomazone, with apparent recovery after a short time. Our results provide useful information on the effects of herbicide residues in aquatic systems. This information can help minimize the risk of long-term reproductive effects in non-target species that have been previously overlooked in ecotoxicology studies.