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The upper part of the Krka River estuary and Prokljan Lake are a specific example of a well-stratified estuarine environment in a submerged river canyon. Here, we reconstructed the geomorphological evolution of the area and classified the data gathered in the study, integrating multibeam echosounder data, backscatter echosounder data, side-scan sonar morpho-bathymetric surveys, and acoustic sub-bottom profiling, with the addition of ground-truthing and sediment analyses. This led to the successful classification of the bottom sediments using the object-based image analysis method. Additional inputs to the multibeam echosounder data improved the segmentation of the seafloor classification, geology, and morphology of the surveyed area. This study uncovered and precisely defined distinct geomorphological features, specifically submerged tufa barriers and carbonate mounds active during the Holocene warm periods, analogous to recent tufa barriers that still exist and grow in the upstream part of the Krka River. Fine-grained sediments, classified as estuarine sediments, hold more organic carbon than coarse-grained sediments sampled on barriers. A good correlation of organic carbon with silt sediments allowed the construction of a prediction map for marine sedimentary carbon in this estuarine/lake environment using multibeam echosounder data. Our findings highlight the importance of additional inputs to multibeam echosounder data to achieve the most accurate results. [ABSTRACT FROM AUTHOR]