Although shrimp larvae are susceptible to many pathogens and water quality and diseases affect commercial shrimp production, the relation between these factors are less studied. Therefore, we aimed to investigate the effect of bacterial dynamics and water quality factors on Penaeus monodon larvae. We recorded the survival rates, water quality (total ammonia, nitrite, and nitrate concentration), heterotrophic bacteria, and vibrios during different P. monodon stages(nauplii, zoea, mysis stage, postlarvae). In ponds 1, 2, 3 and 4, the survival rates were significantly lower but the nitrite concentration and vibrio numbers (before mysis stage) were considerably higher than those in other ponds (P < 0.05), indicating that nitrite and vibrios influenced P. monodon survival during larva culture. Nitrite and nitrate concentrations increased from day 6, and increased dramatically by day 12. Total ammonia concentration increased continuously from day 1 to 15. Heterotrophic bacteria increased slowly in the nauplii and zoea stages, grew rapidly in the mysis stage, and remained almost stable and reduced slightly in postlarvae. In most ponds, vibrio numbers did not change significantly in the nauplii and zoea stages, but increased from the mysis stage and were >10-4 cfu/mL, which potentially cause shrimp disease. Therefore, we suggest that the mysis stage is the key time when water quality and bacteria increase rapidly, and precautions should be taken to improve water quality and inhibit vibrio growth.