Despite laws and directives for the regulation and restriction of pesticide in farming, the large use of Plant Protection Products (PPPs) in paddy fields is a relevant worldwide cause of contamination of the environment. The aim of this work is to evaluate the environmental impact due to the use of PPPs by using an integrated approach based on chemical analyses and ecotoxicological hazard assessment, supported by statistical tools, in order to overcome the issues related to the traditional tabular evaluation. Samples of soil and water of seven conventional and organic paddies located in Northern Italy have been examined for two years by extensive chemical and ecotoxicological analyses. The results evidenced a direct relationship between the presence of Oxadiazon in water and bioassays responses as the main cause of the toxicity measured. This phenomenon affected both biological and conventional rice fields, due to the free circulation of water through irrigation canals. Therefore, the implementation of organic districts with a water circulation isolated from conventional fields represents a simple and effective countermeasure to safeguard the agricultural practices of organic crops.