The aim of this study was to evaluate the effect of a commercial probiotic on the bacterial and phytoplankton concentration in intensive shrimp farming (Litopenaeus vannamei) with a recirculation system, for one culture period in Rio Grande do Norte, Brazil. Ponds, with mean area of 2.6 ha, were stocked with a density of 98 shrimp m-2. A commercial probiotic was prepared following the manufacture's specifications and sprayed on the surface of the ponds seven days prior to stocking and then on a weekly basis until harvest. The same procedures were used with all treatments (control and probiotic), with regard to feeding, liming, fertilization, use of molasses and monitoring of water quality. Field data were analyzed using ANOVA, the Tukey test and Chi-square tests. No significant differences between treatments were found for water quality data, but treatment means showed significant differences for total heterotrophic bacteria in the sediment (5.181 ± 0.34x10(4) cfu g-1 and 5.749 ± 0.67x10(4) cfu g-1), total heterotrophic bacteria in surface water (4.514 ± 0.95x 10(4) cfu m L-1 and 4.136 ± 0.81x10(4) cfu m L-1) and positive sucrose in surface water (2.438 ± 0.72x10(4) cfu m L-1 and 2.203 ± 0.76x10(4) cfu m L-1), respectively, for the control and probiotic treatment. Significant differences were also observed throughout the weeks for total heterotrophic bacteria in the sediment, positive and negative sucrose in the sediment, total heterotrophic bacteria in surface and bottom water, and Pyrrophyta percentage values between 10 and 16 weeks. These results showed that the probiotic causes changes in the total heterotrophic bacteria in the sediment and percentage values of Pyrrophyta concentration, improving the environmental quality of the sediment and water in ponds with closed recirculation systems.