The culture of Penaeus vannamei in inland regions using low salinity water is a reality in several regions of the world. The dissemination of culture techniques that allow high stocking density and reduced water use can be used to optimize the production process, but they require comparative studies to better understand the functioning of these systems in those salinity conditions. Therefore, this study aimed to analyze the effects of different culture systems, which were recirculating aquaculture system (RAS), biofloc technology (BFT), and synbiotic system (Synbiotic) on the water quality, plankton composition, and growth of P. vannamei in low salinity (2 g L−1) and high stocking density (500 shrimp m−3) for 30 days. The shrimp were stocked at a mean weight of 1.27 ± 0.06 g. In the BFT, dextrose was used as the organic carbon source and administered at a carbon: nitrogen ratio of 15:1. In the Synbiotic, rice bran processed by probiotic microorganisms was used as an organic fertilization strategy. In the RAS treatment, all nitrogen species remained stable throughout the trial, without spikes, and with ammonia and nitrate concentrations lower than in BFT and Synbiotic. The BFT treatment had more events when total ammonia nitrogen exceeded 1 mg L−1, requiring water changes. The Synbiotic treatment had better control of nitrogenous compounds, and a more accentuated accumulation of nitrate compared to BFT, suggesting more effective nitrification. The BFT treatment had more microalgae than Synbiotic and RAS. However, the abundance of zooplankton was higher than that of phytoplankton in BFT and Synbiotic, indicating a dominance by heterotrophic organisms. The Synbiotic treatment had a higher abundance of ciliates and amoeba than the other treatments. Furthermore, the Synbiotic treatment provided higher survival, yield, and lower FCR than BFT and RAS. Our findings indicate that the Synbiotic system can be considered as an alternative for the P. vannamei super-intensive culture in low salinity water, as it presented better control of nitrogenous compounds compared to BFT, higher abundance of ciliates and amoeba, and provided better production rates to the culture.