The integrated assessment of ecological risks in farmland was examined by examining the overall connections between the individual risk assessments of pesticides, genetically modified (GM) crops, and weed control. For pesticides, the ecological risks in aquatic ecosystems are assessed using the predicted environmental concentrations of focal pesticides and their acute toxicities to legal test organisms. For GM crops, the ecological risks around farmlands and transportation routes are evaluated based on the substantial equivalence of GM crops to their parental lines. For weed control, management practices are determined mainly by economic acceptance based on weed abundance in and around farmlands, and ecological risks are not addressed at present. Therefore, there is little overlap in assessment items across the three risk factors, and so it seems difficult to integrate the ecological risks by adding the individual assessment results. In order to integrate different risk factors, cost-benefit analyses and multi-criteria decision analyses are often used. However, these analyses have both merits and demerits. For application to decision-making at the field level, it is necessary to set common goals by way of &quot;backcasting&quot; and to integrate risk assessments based on agricultural management practices.