The present work was designed as an extension of a previous study of a barium anomaly observed in stream sediments of the Kupa River. In its upper part the Kupa River drains a region underlain by a trans-boundary aquifer. The river is a significant water resource in a region of tourism, sport, and fishing in both Croatia and Slovenia. The contamination source is situated in Homer (Lokve), Croatia, where barite was mined until 10 years ago. The barium processing waste material (<3-mm fraction) was carelessly deposited in gardens, forests, and into a sinkhole, which has an underground link with the Kupica River, a tributary of the Kupa River. Barium waste and stream sediments were analyzed using comparative techniques: X-ray diffraction (XRD), X-ray fluorescence (XRF), Mössbauer spectroscopy, and grain size analysis. XRD of the waste material identified the major minerals quartz, barite, and dolomite and the Fe-containing minor minerals muscovite and goethite. Barite was identified as a minor or trace mineral in the Kupica River sediments. XRF analysis of the waste material has shown Ba and Fe to be the predominant elements, Ca and K to be minor elements, and Mn, Zn, Sr, Pb, Co, Cu, As, Zr, Rb, Y, and Mo to be trace elements. Mössbauer spectroscopy performed at room temperature (RT) was used to study iron minerals, particularly to obtain information on the valence status of Fe ions. Grain size analysis of the waste material (<63-microm fraction) has shown that it contains 23.5% clay-size material in comparison with 7-8% clay-size material in stream sediments. It is our aim to combine geochemical and medical methods to investigate the possible impact of waste disposal on human health in Lokve. At this stage of the work, concentrations of Ba and other toxic elements in the water compartment of the Kupica River (a source of drinking water) have not been monitored by Croatian Waters (name of the Croatian water authorities). The necessity of such measurements in future studies has been highlighted. A preliminary study of diseases diagnosed in Lokve shows that about 18% of the total inhabitants have serious medical problems. Diseases of the circulatory system, endocrine, nutritional, and metabolic diseases, neoplasms, and respiratory diseases predominate. This paper calls for further multidisciplinary research on the health effects of barium and trace elements, as well as for bioremediation of contaminated gardens and for watershed management of vulnerable karstic aquifers.