Vein-stockwork magnesite in the Madenli area, sedimentary huntite-magnesite in the Asagitirtar area, and lacustrine hydromagnesite in the Salda Lake area are located in the Beysehir-Hoyran and Lycian nappe rocks around Isparta and Burdur, Southwest Anatolia. The aim of this study is to understand trace element contents and carbon-oxygen isotope ratios in different originated magnesite, magnesite bearing huntite, and hydromagnesite deposits. Also, the element contents and isotope ratios of the magnesite occurrences are to compare with each other and similar magnesite occurrences in Turkey and world. It is found that the Madenli magnesite occurrences in the Şarkikaraagac ophiolites, Asagitirtar magnesite bearing huntite deposits in the lacustrine rocks of the Miocene-Pliocene, and the Salda hydromagnesite deposits in lacustrine basin on the Yesilova ophiolites. The paragenesis contains a common carbonate mineral magnesite, less calcite, serpentine, smectite, dolomite, and talc in the Madenli magnesite occurrences, mostly huntite and locally magnesite, dolomite, calcite, illite, quartz, and smectite in the Asagitirtar huntite-magnesite occurrences, and only hydromagnesite mineral in the Salda Lake hydromagnesite occurrences. Vein and stockwork Madenli magnesite deposits were recognized by higher total iron oxide concentrations (mean 1.10 wt%) than sedimentary Asagitirtar magnesite bearing huntite (mean 0.13 wt%) and lacustrine Salda hydromagnesite (mean 0.22 wt%) deposits. It is suggested that high Fe content (up to 5%) in the magnesite associated with ultramafic rocks than those from sedimentary environments (≤1% Fe). Based on average Ni, Co, Ba, Sr, As and Zr contents in the magnesite deposits, average Ni (134.63 ppm) and Co (15.19 ppm) contents in the Madenli magnesite and Salda hydromagnesite (36.85 ppm for Ni, 3.15 ppm for Co) have higher values than Asagitirtar huntite + magnesite (7.67 ppm for Ni and 0.89 ppm for Co). Average Ni-Co contents of these deposits can have close values depending on ophiolite host rock. Average Ba values of the Madenli (108.09 ppm) and Asagitirtar (115.88 ppm) areas are higher than those of Salda hydromagnesite (13.15 ppm). Sediment-hosted Asagitirtar magnesite-huntite deposits have the highest Sr contents (mean 505.81 ppm) as reasonably different from ultrabasic rock-related Madenli magnesite (mean 38.76 ppm) and Salda hydromagnesite (mean 36.70 ppm). The highest Sr content of sedimentary Asagitirtar deposits reveals that Sr is related to carbonate rocks. As and Zr contents have the highest average values (As 52.76 ppm and Zr 9.67 ppm) in the Asagitirtar deposits different from Madenli magnesite (As 0.54 ppm and Zr 1.67 ppm) and Salda hydromagnesite (As 0.5 ppm and Zr 2.58 ppm) deposits. High As and Zr concentrations in the Asagitirtar magnesite-huntite deposits may come from volcanic rocks in near country rocks. The δ 13C (PDB) isotope values vary between −10.1 and −11.4‰ in the Madenli magnesite, 7.8 to 8.8‰ for huntite, 1.7 to 8.3‰ for huntite + magnesite and 4.0‰ for limestone + magnesite in the Asagitirtar huntite-magnesite deposits, and 4.4 to 4.9‰ for Salda Lake hydromagnesite. The sources of the CO2 are hydrothermal solutions, meteoric waters, groundwater dissolved carbon released from fresh water carbonates and marine limestone, soil CO2, and plant C3 in the Madenli magnesite, and may be deep seated metamorphic reactions in limestone and shales of rich in terms of organic matter. The sources of CO2 in Asagitirtar huntite and Salda hydromagnesite were meteoric water, groundwater dissolved inorganic carbon, fresh water carbonates, and marine limestone. The δ 18O (SMOW) isotope composition ranges from 26.8 to 28.1‰ in the Madenli magnesite, 30.4 to 32.4‰ for huntite and 29.8 to 35.5‰ for huntite + magnesite and 26.9‰ for limestone + magnesite in the Asagitirtar area, and 36.4 to 38.2‰ in the Salda Lake hydromagnesite. The Salda Lake hydromagnesite has heavier oxygen isotopic values than others. The sources of oxygen in the Madenli magnesite deposits are hydrothermal solutions, meteoric water, freshwater carbonates, and marine limestone, but the sources of oxygen of the Asagitirtar magnesite-huntite are meteoric water, fresh water carbonates, and marine limestone. The Salda Lake hydromagnesite has very high δ18O isotope values indicating a strong evaporitic environment. Magnesium (Mg+2) and silica are released by disintegration of very weathered-serpentinized ultrabasic rocks of all magnesite deposits and from partly dolomite and dolomitic limestone in the Asagitirtar magnesite bearing huntite deposits. In the Asagitirtar area, calcium (Ca+2) for huntite mineralization is provided by surrounding carbonate rocks. Based on isotopic data, host rocks, petrographic properties of the Madenli magnesite can be described as an ultramafic-associated hydrothermal vein mineralization corresponding to “Kraubath type” deposits, but Asagitirtar ve Salda Lake deposits are sedimentary mineralization (lacustrine/evaporitic) corresponding to “Bela Stena type” deposits. The estimated temperature using average δ18O isotope values is about 33.51 °C for Madenli magnesite, 48.33 °C for Asagitirtar huntite-magnesite, and 25 °C for Salda hydromagnesite. Based on isotope data, we can be say that the Madenli magnesite, Asagitirtar magnesite-huntite, and Salda hydromagnesite occur at low to moderate-low temperature water and alkaline (pH 8.5–10.5) under surface or near-surface conditions.