The use of saline-alkaline water for aquaculture has become a notable method for the comprehensive utilization of water and land resources in saline-alkaline soil. Litopenaeus vannamei is an important species in saline-alkaline aquaculture. The microbial community in water plays an important role in aquaculture processes. However, the dynamic changes of bacterioplankton throughout the entire process in shrimp farming ponds in saline-alkaline soil should be investigated to reveal the microbiota characteristics. In the present study, 16S rRNA high-throughput sequencing technology and Illumina MiSeq sequencing platforms were used to analyze the bacterioplankton in the water samples from saline-alkaline L. vannamei aquaculture ponds in the Hetao Plain of Inner Mongolia. Forty-three phyla and 1004 bacterial genera were detected in samples collected at seven time points. Firmicutes (33.82%), Proteobacteria (25.82%), Cyanobacteria (17.36%), and Actinobacteria (17.36%) were the phyla with more than 10% abundance and they showed significant differences between different samples. At the genus level, the dominant genera were Exiguobacterium, Psychrobacter, and Cyanobium_PCC-6307 and their abundance were significantly different among all groups. Exiguobacterium were enriched during the early and middle stage (0–30 d, 19.57%–55.17%), with less relative abundance during the later stage (40–60 d, 13.32%–24.84%). Psychrobacter was less abundant on Day 0, Day 10, and Day 40 (0.07%–0.53%); however, its relative abundance increased notably on Day 50 (49.21%). Cyanobium_PCC-6307 showed an increase in abundance on Day 40, with small fluctuations in the remaining samples (3.87%–13.12%). Planococcus had the highest relative abundance in the water before the release of shrimp (9.68%) and decreased during the later culture stage. Massilia and Chryseobacterium were specifically enriched only on Day 30. Cyanobacteria could be considered as the major threat in inland saline-alkaline water aquaculture, with a low abundance of Vibrio. Exiguobacterium and Psychrobacter can be considered as the chief probiotics in the water source and saline-alkaline pond because of their ability to inhibit the bloom of Cyanobacteria. Unique bacterioplankton communities were formed in different aquaculture stages, with water temperature and nitrogen and phosphorus nutrients driving the succession of bacterioplankton communities.