In the method, there is manufactured a poorly water permeable mineral sealing structure by forming a material layer (104) of a sealing material containing reactive binding agent and by allowing the layer to strengthen into a so-called synthetic hardpan layer. The strengthening material layer is formed of a sealing material, at least a part of which is waste fraction generated in the concentration process of the mining industry, such as so-called tailings or deposit, which is processed thermally to enhance the reactive characteristics of the waste fraction. The sealing structure can be a sealing structure of a tailings pond of the mining industry, waste rock heap, solid waste heap forming in the ore extraction process, or a sealing structure for a foundation or surface structure of a deposit basin or a sealing structure for an edge dam of a tailings pond or deposit basin.