Four long marine sediment cores (3,5-to 6,5 m) were sampled in the semi-enclosed bays of Novigrad and Karin Sea and Velebit channel, in locations at Zrmanja river mouth (named ZRM-A), Novigrad Sea (NOV-3), Karin Sea (KAR-A) and Modrič bay (MOD-A). Fifteen soil sediment cores or profiles were sampled in their respective catchments. Marine sediments span over the last 11.500 yr. Three marine sediment cores penetrated the marine sediment sequences and terminated in terrestrial sediments predating the Holocene flooding by the Adriatic Sea. The core at the mouth of Zrmanja river estuary covered a 4.500 yr. sequence of marine sediments. The main objective of this study is to outline the Holocene palaeo-environmental evolution (last 11.500 years) in catchments. Environmental changes in the catchments were determined by high resolution analysis using multi-proxy approach comprising chemical analysis (including C/N), particle size analysis, bulk and clay mineralogical XRD analysis, magnetic susceptibility (MS) and remanent magnetism analysis, and L*a*b* spectrum. To determine the age of the sediments, Carbon–14 (14C AMS) and Cesium-137 (137Cs) isotopes were used. Results were analysed using multivariate statistical methods and GIS modelling of catchment evolution. Spatial distribution of determined sequences was determined in geoacoustic underwater survey using side scan sonar, echosounder and subbottom profiler. Seismic data shows river channels incised in Pleistocene clastic rocks that existed during early Holocene. Larger channel, flowing from Karin Sea into Novigrad Sea was connected to river Zrmanja flow, and flew further through Novsko ždrilo into Velebit channel. Seismic data points to existence of braided river system. Larger depressions and irregular erosional forms were filled with freshwater or later brackish sediments. Marine cores NOV-3 and MOD-A terminated in terrestrial sediments predating the Holocene flooding by the Adriatic Sea. In the NOV-3 core terrestrial sediments occur after 10.750 cal. yr. BP, in MOD-A after 10.210 cal. yr. BP, and in KAR-A at 9.870 cal. yr. BP. Determined dates of marine transgression into semi-closed bays fit well with current relative sea-level curves for Adriatic. The shallow and isolated Karin Sea bay (15 m deep) shows evidence of a brackish lake/marsh system in the period from 7.480 to 8.500 cal. yr. BP. It is recognized by high Ca concentration, low Sr/Ca ratio, elevated Sr/Ba, Pb/Al, Mg/Al ratios, elevated C/N, pollen and foraminiferal assemblages. High Ca concentrations and low siliciclastic input typical for karstic lake sedimentation is also visible in core NOV-3 until 10.140 cal BP. This period is followed by sedimentation of fine grained dominantly silty sediments with dominance of calcite and quartz. Dark, low MS sediment with low TOC, C/N, Sr/Ca, Mg/Al and Mn/Fe ratios is typical for marine sedimentation, which lasts until today. Thickness of Holocene marine sediments according to subbottom profiler data is up to 16,5 m in Novigrad Sea and up to 9 m in Karin Sea. River Zrmanja delta has up to 27 m of deposits down to klastic base. Younger parts of the sediment cores recovered from the enclosed bays show marine sediment influenced by the terrestrial supply in the last 1.900 years. Evidence of anthropogenic changes with pronounced erosion due to deforestation in the subcatchments is evident in all marine cores as elevated χlf, χfd(%), changes in color (influx of red terra rossas visible as high a* and b*), elevated Pb, lithogenic elements, TOC, C/N and decreased carbonates. Indicators of anthropogenic influence occur at different periods in the subcatchments due to different periods of settlement. The earliest anthropogenic impact (deforestation and erosion) is visible in river Zrmanja mouth at 1.880 cal BP followed by Modrič bay at 1.715 cal BP, and 715 cal BP in Karin sea. Significant influx of terrigenous material is visible from 720 cal BP at ZRM-A, 515 cal BP in KAR-A and 240 cal BP in MOD-A. Highest erosion period in all three locations is similar, and lasts from 160 to 265 cal BP. Similar event is evident in Krupa river floodplain (Zrmanja catchment), where high organic peat-like sedimentation is sharply replaced by high terrigenous input due to deforestation in the surrounding slopes at 1.875 cal BP. Heavy metal concentrations increase at the same time as the increase in terrigenous input. Normalizing heavy metal concentrations with Al concentration showed anthropogenic influence is evident only for Pb and Cu, and it lasts from 1.400 cal BP, while increased pollution is visible in last 150 years. Concentrations of Ni, Zn and Mn show natural variations in concentrations with no visible human influence. Analysis of clay content and ratios Cr/Al vs Ni/Al and V/Al vs Ni/Al in soil sediments from adjacent catchments was used to determine possible sources of marine sediments. Clay minerals in core KAR-A are similar to cores 508/T and 508/F. Core ZRM-A in river Zrmanja mouth has two different sources of sediment. Sediment in the upper 160 cm has clay composition similar to Krupa catchment sediments, while sediment in the lower part of the core is similar to Žegarsko polje and upper Zrmanja catchment sediments. Sediments in NOV-3 located in the deep part of Novigrad Sea are similar to lower parts of KAR-A marine sediment core and soils from Karin Sea catchment.