A combined inorganic and organic geochemical study was carried out on marls and mudstones collected from the Lower Miocene Lopare Basin, Bosnia and Herzegovina. A total of 46 samples collected from two boreholes, Pot 1 (depth of 193 m) and Pot 3 (depth of 344 m), showed that element abundances like boron (B), lithium (Li), strontium (Sr), uranium (U), chromium (Cr), nickel (Ni), magnesium (Mg), sodium (Na) and calcium (Ca) are much higher than average than in the upper continental crust (UCC). Chemical composition indicates at least two sources: (i) Mesozoic ophiolites occurring in the north of the investigated area, and (ii) dacito-andesitic pyroclastics (Mesozoic to Cenozoic). Lopare Basin sedimentation was influenced by strong evaporation resulting in a partly hypersaline lake, which formed during a warm climatic period, probably during the Miocene Climatic Optimum. A brief episode of humid climate conditions resulted in the basin filling-up and deposition of felsic sediments enriched in thorium (Th). Organic geochemistry shows that the majority of studied sediments contains predominantly immature to marginally mature algal organic matter (OM). The biomarker patterns are generally in agreement with the geological history of the Lopare Basin and inorganic and mineralogical data. Conversely, the molecular distribution of n-alkanes as reliable climatic and δ-MTTC as paleosalinity indicators do not support this conclusion.