The negative influence of agrochemicals (pesticides: insecticide, fungicide, and herbicide) on biodiversity is a major ecological concern. In recent decades, many insect species are reported to have rapidly declined worldwide, and pesticides, including neonicotinoids and fipronil, are suspected to be partially responsible. In Japan, application of systemic insecticides to nursery boxes in rice paddies is considered to have caused rapid declines in Sympetrum (Odonata: Libellulidae) and other dragonfly and damselfly populations since the 1990s. In addition to the direct lethal effects of pesticides, agrochemicals indirectly affect Odonata populations through reductions in macrophytes, which provide a habitat, and prey organisms. Due to technical restrictions, most previous studies first selected target chemicals and then analyzed their influence on focal organisms at various levels, from the laboratory to the field. However, in natural and agricultural environments, various chemicals co-occur and can act synergistically. Under such circumstances, targeted analyses might lead to spurious correlations between a target chemical and the abundance of organisms. To address such problems, in this study we adopted a novel technique, “Comprehensive Target Analysis with an Automated Identification and Quantification System (CTA-AIQS)” to detect wide range of agrochemicals in water environment. The relationships between a wide range of pesticides and lentic Odonata communities were surveyed in agricultural and non-agricultural areas in Saga Plain, Kyushu, Japan. We detected significant negative relationships between several insecticides, i.e., acephate, clothianidin, dinotefuran, flubendiamide, pymetrozine, and thiametoxam (marginal for benthic odonates) and the abundance of lentic Epiprocta and benthic Odonates. In contrast, the herbicides we detected were not significantly related to the abundance of aquatic macrophytes, suggesting a lower impact of herbicides on aquatic vegetation at the field level. These results highlight the need for further assessments of the influence of non-neonicotinoid insecticides on aquatic organisms.