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Exploring the relationship between evaporation (E)-minus-precipitation (P) and sea surface salinity (SSS) is vital for understanding global hydrological cycle changes and investigating the salinity budget. This study quantifies the uncertainty in the relationship between E−P and SSS based on satellite data over the 50°S–50°N ocean from 2012 to 2017 in 140 sets of combinations of E, P and SSS. We find that the uncertainty (10%) in the variability of freshwater flux (FWF) over 2012–2017 is smaller than that in SSS (15%). The difference in the combination of sets of “E-P-SSS” products can lead to the 10% difference in RMSD and 25% difference in area-weighted mean correlation coefficients between SSS tendency and FWF. There is a 24.1~58% area over the global ocean with a significant (p value < 0.05) positive correlation between the FWF and SSS tendency derived from satellite products. The seasonal EMP and SSS tendencies show larger correlation coefficients and lower RMSDs over most sets compared with those on nonseasonal time scales. Large uncertainty in the FWF-SSS tendency relation associated with spread among products prevents the use of one combination of E, P and SSS from satellite-based products for salinity budget analysis.