The rice production in Indonesia is dominated by permanent flooding or inundation system. Intensification of permanent flooding of paddy soils not only reduces the soil biological power significantly, but also restricts the roots growth. Various field studies indicated mostly of paddy soils in Indonesia has a low organic content (< 2%). Management of paddy soil health is urgently required to restore, improve and maintain the soils organic matter as heart of soil ecosystem. SOBARI (system of organic based aerobic rice intensification) as water saving technology combined with straw compost based fertilizers technology has two main goals: (1) to remediate or restore, improve and maintain the health and quality of paddy soils, and (2) to enhance rice productivity in sustainable ways (efficient water and fertilizer use). The field results using several rice varieties in Indonesia revealed that the water saving technology combined with organic fertilizers (straw compost) can produce grain yield about 8 – 12 t/ha (average of an increasing about 50 – 150% compared to anaerobic rice cultivation) and the water irrigation was reduced by at least 30 - 50% and as well as inorganic fertilizers was reduced at least by 25% This high rice yield is highly correlated with the increasing of roots zone about 4 – 10 times, number of productive tillers about 60 – 80 tillers, number of panicles, length of panicles and number of grain/panicle, and as well as due to the increase of soil biodiversity. The reuse of straw or straw compost into soils within three years is expected to be able to remediate and improve the health of degraded paddy soils significantly.