Novigrad Sea is a small bay of the Adriatic Sea in which northeastern part Zrmanja River discharges and forms highly stratified estuary. Investigation of geochemical, sedimentological and mineralogical characteristics of sediments of wider area of the Novigrad Sea was conducted in order to determine the origin of the material, the deposition conditions as well as natural and anthropogenic factors of influences on sedimentation in the Novigrad Sea. The results showed that the composition of the Novigrad Sea sediments is primarily determined by natural factors, although sporadically we find the impact of anthropogenic activities. Composition of the investigated sediments is influenced by geological background, hydrodynamic conditions, biogenic production as well as the physico-chemical processes that govern the yield of dissolved and particulate phases of the Zrmanja River and Karišnica River and coagulation of colloidal materials along the salinity gradient. Material brought by Zrmanja River partly deposits on the mouth of the river in the Novigrad Sea while the material in suspension deposits in the deeper parts of the basin. Reoxidation of metal oxides at the water-surface interface makes Novigrad Sea sediments place of trace element disposal. Most of the material brought by River Zrmanja and River Karišnica deposits within the Novigrad Sea and the Karin Sea area. The composition of the Zrmanja River sediments indicates the impact of the ex-alumina factory Jadral and transfer by wind of the material from its immediate proximity to the water system of the Zrmanja River. The composition of surface and bottom water of the Novigrad Sea area reflects the geological and hydrogeological background, while the distribution of trace elements in the water column is determined by salinity and remobilization of elements from the sediment into the water column.