Organic farming is attracting attention as an agriculture that brings the agriculture ecosystem to life. This study assessed the effect of herbicide on aquatic oligochaetes in paddy and estimated the loss of ecosystem function sustained by oligocheaeta. Field surveys of oligochaete were conducted between June 2010 and May 2011 and the community was dominated by Limnodrilus hoffmeisteri and Branchiura sowerbyi. Laboratory incubation revealed that these two species translocated lower sediment soil to surface, and increased NH₄⁺ concentration of paddy water in density dependent manner. Toxicity test on PCP (the most popular herbicide in Japan in the 1960s and the 1970s) was conducted for these oligochaeta species and a standard test species (Lumbriculus variegatus). Regular dose of PCP was 140mg/kg soil. This value was higher than both EC₅₀ and LC₅₀ for B. sowerbyi. Therefore we estimated that during the period of applying PCP, the ecosystem functioning by aquatic oligochaete has been lost at least 50% for soil translocation and 25% for nitrogen cycling.