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The use of organic manures as an alternative to chemical fertilizers is an option for the development of sustainable farming systems in Japan. The present study examined the effect of rapeseed oilcake (RO) not only on yield and yield components of rice (Oryza sativa L.) but also on soil fertility parameters and surface water quality in a paddy field by comparing them with the effects of conventional inorganic fertilizer (IF) and a control (CR), that is, natural (unfertilized) system. The long-term field experiment from 1990 to 2006 demonstrated the indigenous sustainability of paddy systems, because husked grain yield and shoot biomass in the CR plot remained at moderate levels (ave. 323 ± 56 g m-2 and 843 ± 166 g m-2, respectively) over 17 successive years. Meanwhile, the application of RO comparatively improved grain yield (ave. 538 ± 83 g m-2) and shoot biomass (ave. 1478 ± 187 g m-2) to almost the same level as with IF (ave. 538 ± 68 g m-2 and 1511 ± 173 g m-2, respectively) during the study period. Soil fertility assessment in the last experimental year (2006) indicated that RO could improve the soil quality to the same extent as IF because major fertility parameters showed similar values between the RO and IF plots. On the other hand, the application of IF induced a substantial increase in estimated load outflows of nitrogen (N) and phosphorus (P) from the paddy surface water (2.46 g N m-2; 0.38 g P m-2) as compared to the CR plot (0.92 g N m-2; 0.06 g P m-2). Outflows from the RO plot showed relatively lesser effluent loads (2.00 g N m-2; 0.14 g P m-2) than the IF plot. From the findings of this study, we concluded that RO is agronomically similar to but an environmentally better resource material than conventional IF in the lowland rice farming system in Japan. [ABSTRACT FROM AUTHOR]