Virgin olive oil (VOO) is a functional food specific to the Mediterranean diet and related to human health, especially as a protector of cardiovascular health, in the prevention of several types of cancers, and in modification of immune and inflammatory response. Phenolic compounds have central importance for these extraordinary health benefits. In the production of high-quality olive oils, it is very important to process freshly picked olives and avoid any storage of fruits. However, in Croatia there is a very traditional and environmentally friendly method of olive oil production, where olive fruits are stored in seawater for some time prior to processing. This practice is also notable nowadays since there are people who prefer the characteristic flavor of the “seawater olive oil”, although some people argue against its quality and biomedical relevance. In this study, the phenolic contents of VOO prepared from the immediately processed fresh olives and olives processed after storage in seawater were compared with the use of high-performance liquid chromatography-mass spectrometry (HPLC-MS) and spectrophotometric analysis. The results suggest that “seawater olive oil” should be considered as a safe food of biomedical relevance, as it still contains a significant proportion of important phenolics like hydroxytyrosol, tyrosol and oleacein (e.g., 63.2% of total phenols in comparison to VOO).