This study presents a chemometric protocol for the determination of site-specific elemental and strontium isotopic fingerprints in sturgeon caviar. The elemental and strontium isotopic composition of water, fish feed, salt, raw (i.e., unsalted) and salted sturgeon caviar samples from six fish farms in Europe and Iran was determined by (multi-collector) inductively coupled plasma mass spectrometry ((MC) ICP–MS). Multiple linear regression revealed six site-specific markers absorbed from water into sturgeon caviar (n(87Sr)/n(86Sr) isotope ratio and content of Na, Mn, Cu, Mo, Fe/Ca). Salting changed the chemical composition of four (n(87Sr)/n(86Sr), Na, Mn, Fe/Ca) of the six site-specific markers significantly. Washing of salted caviar could not fully remove the influence of salt on the affected site-specific markers. Therefore, a novel mathematical procedure based on mass balance calculations was developed for determining the n(87Sr)/n(86Sr) isotope ratio absorbed from water into sturgeon caviar. The resulting variable is an estimate for the environmental strontium isotopic signal and independent of the production process. Hierarchical cluster analysis showed that the combination of the mathematically determined n(87Sr)/n(86Sr) isotope ratio of water in sturgeon caviar and two site-specific markers, which were not affected by salting (Cu, Mo), allowed differentiating salted caviar samples from six fish farms into five distinct clusters. The proposed combination of statistical and mathematical tools provides the basis for origin determination of salted sturgeon caviar using site-specific elemental and strontium isotopic fingerprints, even in cases where the initial environmental signature was altered by the production process.