Balneotherapy (BT) is one of the most commonly used complementary therapies for many pathological conditions. Its beneficial effects are related to physical and chemical factors, but the exact mechanism of action is not fully understood. Recently, there has been an increased interest in the use of preclinical models to investigate the influence of BT on inflammation, immunity, and cartilage and bone metabolism. The objective of this comprehensive analysis was to summarize the current knowledge about the in vitro studies in BT and to revise the obtained results on the biological effects of mineral waters. Special attention has been paid to the main rheumatological and dermatological conditions, and to the regulation of the immune response. The objective of this review was to summarize the in vitro studies, on human and animal samples, investigating the biological effects of BT. In particular, we analyzed the properties of a thermal water, as a whole, of an inorganic molecule, such as hydrogen sulfide in different cell cultures (keratinocytes, synoviocytes, chondrocytes, and peripheral blood cells), or of the organic component. The results corroborated the scientific value of in vitro studies in demonstrating the anti-inflammatory, antioxidant, chondroprotective, and immunosuppressive role of BT at the cellular level. However, the validity of the cell culture model is limited by several sources of bias, as the differences in experimental procedures, the high heterogeneity among the available researches, and the difficulties in considering all the chemical and physical factors of BT. We would like to stimulate the scientific community to standardize the experimental procedures and enhance in vitro research in the field of BT.