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Rice cultivation in Java has been practiced for centuries. The long and complicated practices undoubtedly had given birth to synergistic cultivating traditions between farmers and their environment. The drastic and revolutive changes happened in the second half of the twentieth century. Introduction of external synthetic inputs such as fertilizers and pesticides, which was first thought as very helpful in increasing yield and production, is right now reconsidered as negatively affecting rice agroecosystem as a whole. Those inputs inhibited and even destroy natural agroecosystem services. The proofs came from rice herbivore population increase, which happened several times during these changing times. The right practices in coping with rice herbivore or diseases should have been made available. To emphasize the role of ecosystem services, we tried to investigate whether ecosystem basic rules had been violated, and to find out, if the ecosystem services were improved, whether they will help maintain ecosystem balance. Therefore we design experiments to know how far the rice cultivation practices have been affected by the change in ecosystem services, especially in preventing and controlling biological disturbances. First, we tried to know whether mono-culture practices might be improved by using different rice varieties and mixed them prior to planting. Secondly, we practiced crop rotation by interfering continuous all year round rice planting by introducing dry land crops such as corn during the dry season, although the irrigation water was available. And third, we planted refugias around the rice planting area where the refugias were never before planted in the area. All experiments were quantitatively analyzed, and compared to the traditional or conventional practice done by the farmers. The result shows that these practices more or less improved the conventional rice agroecosystem. Mixing varieties resulted in more preferable rice production in term of performance, including taste. The interference of dry land crop, i.e. corn, invite rat, a more destructive herbivore. The planting of refugias increase the number of beneficial arthropod although an ecological equilibrium is still yet to be observed. The adjustment of these practices to the rice environment had not yet commonly done, since what is commonly known as sustainable agriculture was not intensively encouraged. The rice production system is still based on maximum yields and the achievement of self-supporting regions. Understanding of proper practices to ensure the sustainability of rice cultivation should be disseminated among stakeholders.