This research is aimed to assess the effect of salinity stress on bacterial density on simulation system for salt water intrusion. The study consisted of 5 treatments with different salinities at 0, 10, 20, and 30‰, respectively, which were diluted from brine water, and seawater 32‰ (B32‰). Each treatment was triplicated and monitored in 50 days. The outdoor experiment was designed randomly in 500 L composite tanks. The microbial parameters of sediments such as total heterotrophic bacteria, Bacillus spp., Lactobacillus spp., Vibrio spp., Vibrio parahaemolyticus was evaluated every two weeks. The results show that total heterotrophic bacteria redued in high salinity. Total heterotrophic bacterial density was highest at 6.2 Log CFU/g in treatment of 0‰ while the lowest density in seawater treatment (B32‰), approximately 5.7 Log CFU/g. The density of Bacillus spp. reduced under high salinity and reached a peak at a salinity level of 10‰ and 0‰. In addition, the highest density of Lactobacillus spp. was counted in treatment of 10‰ (3.05 Log CFU/g) and significantly difference from other treatments (p<0.05). The Vibrio, and V. parahaemolyticus density considerably fluctuated by the different salinity levels. The results indicate that the density of Vibrio and V. parahaemolyticus in 20‰ and 30‰ treatment was significantly higher than those obtained in the comparison groups (p<0.05).