Low oxygen (hypoxia) and elevated CO2 (hypercapnia, are characteristic of estuarine environments. Although hypoxia and hypercapnic hypoxia decrease the resistance of shrimp to bacterial pathogens, their direct effects on the immune system are unknown. Here we present evidence demonstrating in the penaeid shrimp Litopenaeus vannamei that both hypoxia and hypercapnic hypoxia affect the localization of bacteria, their conversion from culturable to non-culturable status (bacteriostasis), and their elimination from hemolymph and selected tissues. Shrimp were injected with a sublethal dose of a pathogenic strain of Vibrio campbellii expressing green fluorescent protein and resistance to kanamycin. Real-time polymerase chain reaction was used to determine the number of intact V. campbellii in hemolymph, gills, hepatopancreas, heart, and lymphoid organ. Selective plating was used to quantify the injected bacteria that remained culturable. We found that both hypercapnic hypoxia and hypoxia increased the percentage of culturable bacteria recovered from the hemolymph and tissues, suggesting an overall decrease in bacteriostatic activity. Hypoxia and hypercapnic hypoxia generally increased the distribution of intact V. campbellii to the hepatopancreas and the gills, which are major targets for the pathogenic effects of Vibrio spp., without affecting the number of intact bacteria in the lymphoid organ, a main site of bacterial accumulation and bacteriostatic activity.