The aim of this study was to analyze the influence of organic fertilizer on the availability of natural food (plankton and benthos) and water quality. Two fertilization protocols were adopted using inorganic and organic fertilizers with shrimp (stocked treatment) and their controls (unstocked treatment). Experimental units consisted of 12 circular fiberglass tanks (500 l) with estuarine sediment, individual aeration and no water exchange. In stocked treatments were used 40 juveniles/m², and they were fed with 35% crude protein marine shrimp ration, three times a day. Under the organic fertilization protocol, the plankton showed higher abundance of Nitzschia and rotifers, the phytobenthos consisted mainly of Nitzschia, Amphiprora and Oscillatoria, the epibenthos was represented mainly by nematodes and rotifers, and the macro-invertebrates were mainly oligochaetes. In relation to inorganic fertilization, the plankton was represented mainly by Coscinodiscus and rotifers, the phytobenthos consisted mainly of Amphiprora and Oscillatoria, the epibenthos was represented mainly by nematodes and rotifers, and the macro-invertebrates were mainly oligochaetes. Dissolved oxygen was higher for organic fertilizer (6.16 ± 0.98 mg/l) than for inorganic (5.92 ± 1.19 mg/l) while the other water quality parameters did not present significant differences. Survival was similar in the two fertilization regimes (96.6%). Final body weight was 11.89 ± 1.73 g for the inorganic fertilizers and 12.28 ± 1.71 g for organic fertilizer. It is concluded that wheat bran showed good performance in the water quality without exchange, in the availability of natural food, and in the growth and survival of the shrimps in the microcosms.