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Formation water salinity is a key parameter to determine water saturation (Sw) from resistivity logs, and, consequently, to estimate initial volume of hydrocarbon in place. Ideally, salinity is directly measured from water samples collected within the producing interval, however, such samples are not always recovered during drilling and, even when available, contamination from drilling mud or completion fluids can prevent measuring the correct salinity. Here, we present a fluid inclusion technique to measure salinity that can be used as input for Sw calculation. We apply this technique to two Lower Miocene gas reservoirs in the southwestern Pannonian Basin across the Hungarian-Croatian border. In Reservoir A, the latest assemblage of secondary inclusions was trapped in quartz approx. 200 ka. Salinity of the aqueous fluid trapped in the secondary inclusions is approx. 15–20 ppt which is interpreted to represent the same salinity of present-day formation water. Such measurements allowed us to greatly reduce uncertainty of salinity value for Sw calculation. Reservoir B, in which salinity is known from reservoir fluid samples, was used as testing case. Here, salinity of the latest secondary inclusions in quartz overgrowth ranges from 49.6 to 60.1 ppt which overlaps with salinity measured from reservoir flow test spanning from 45 to 60 ppt. Our study shows that fluid inclusion analysis is a valuable tool for reducing salinity uncertainty in gas reservoirs when calculating Sw with resistivity-based methodology.