This study was conducted to establish the pilot-scaled ponds that farming managements was operated in accordance with the written standards for organic aquaculture. Three treatments each in replicate of two were conducted. In organic pond, the stocking density was 0.20 kg/m2. Fish were fed on the diet with organic feedstuffs. In organic ponds with additional plastic substrates, the plastic nets or sacks were introduced into the water column. Fish were fed on the organic diet at 70% amount of the organic treatment. Two concrete ponds at stocking density 0.36 kg/m2 were served as control, where the fish were fed on the diet with regular feedstuffs. For the formulation of organic feed for tilapia, 10% soya pomace can be added to the feed without adverse effects on growth and feeding of tilapia. The results of 18-week farming trial showed that final weight, percent weight gain and specific growth rate were not significantly different among treatments. However, feed utilization of fish in organic ponds with additional plastic nets or sacks were better than that of the control pond. On the other hand, the dry matter and chlorophyll-a of periphyton on the plastic sacks were higher than that of the plastic sacks. For water quality, lower nitrogenous waste concentrations in the water column were recorded in the presence of periphyton compared with controls that did not have substrates. In this way, the decrease of organic feed input and reduction of production costs could be achieved under the restrictions from organic regulations.