The identification, characterisation and formation of manganese minerals takanelite and kutnahorite calcian found in the Krka River Estuary, is described. These minerals originated from the hydrochemical transformation of waste disposed from a ferromanganese factory. Industrial slag, dust settled inside a chimney, and marine sediments in the vicinity of the ferromanganese plant ''Crnica'', situated in the suburb of the city of Sibenik were analysed in details. The samples of slag and dust were equilibrated with estuarine waters for 20 d. In marine sediment, calcite is predominant, while quartz, aragonite, kutnahorite calcian and dolomite were found as minor components. Iron is present in all samples as an amorphous phase. Strontium, titanium, copper, zinc, lead and rubidium were found as microcomponents. It was found that slag and dust particles partly dissolve in contact with estuarine water of different salinities, and present renewable supply of manganese, iron and numerous trace elements. A possible way of the formation of manganese minerals takanelite and kutnahorite is discussed. Takanelite mineral was obtained in laboratory by partial disolution of slag containing bustamite ferroan. For kutnahorite calcian it is suggested that it forms in the process of dolomitization; With respect to aqueous environment of the Krka River Estuary, the slag and dust from a ferromanganese industry upon contact with water transform into scavengers (gypsum, calcite, quartz, takanelite) which help purifying the water column from other micro-impurities.