Recent studies have revealed widespread brackish, low-salinity conditions across the Yangtze Subprovince of South China during the Cambrian Explosion, highlighting the potential importance of salinity in shaping the ecological distribution of early marine faunas. To explore this further, we reconstructed the paleosalinity of the exceptionally preserved fossil Lagerstätte—the Qingjiang Biota, using B/Ga and B/K ratios data from two borehole sections at key fossil localities. Both B/Ga and B/K ratios demonstrate a consistent up-section decreasing trend from the base of Cambrian Stage 3 into the biota-bearing interval, with B/Ga decreasing from ~12 to ~8 and B/K from ~70 to ~60. These results indicate a gradual decline of the salinity from near open-ocean conditions to lower, yet still fully marine levels during this period. Integrated with published salinity data, the spatial distribution pattern suggests that the study area possibly received freshwater input from the northwest and open-ocean seawater from the northeast. We propose that the distinctive hydrological regime maintained long-term normal marine salinity conditions that fostered the ecological proliferation of the Qingjiang Biota. These findings advance our understanding of paleosalinity variations on the Yangtze Subprovince and underscore the role of salinity in shaping ecological dynamics during the Cambrian Explosion.