Ecological risk management of pesticides in Japan is based on the ecological risk assessment for a model aquatic ecosystem using the predicted environmental concentrations of focal pesticides and their acute toxicities to legal test organisms, but the uncertainty of this assessment has been pointed out. To improve the assessment reliability, the effect of pesticides on a real ecosystem should be addressed based on field data. Therefore, we conducted a multi-point monitoring of aquatic plants and rice herbicides in agricultural ditches around paddy fields in central Japan, and found that submerged plants such as Potamogeton crispus L. were indicator species to detect the adverse effect of rice herbicides, and a rice herbicide, bensulfuron-methyl (BSM) had a significant ecological risk for the submerged plants. However, we also found that the acute toxicity of BSM was comparable to other rice herbicides by exposure experiments using P. crispus in a controlled laboratory condition. These findings suggest that the ecological impact of rice herbicides on aquatic plants can be identified using field data, but it reflects the locality of herbicide use in the field. Thus, heterogeneous use of pesticides among fields and regions should be taken into account to assess the ecological risk of pesticides based on the field data.