Confined shallow-water environments are encountered many places along the coast of the inner Danish waters. Most of these water bodies are spatially constrained within the moraine topography left by the last glaciation of Scandinavia. Despite their common occurrence, coastal lagoons have rarely been studied as sedimentary archives. In this study we set out to trace back changes in relative sea-level and associated geomorphological responses of the coastal environment in sediment cores retrieved from lagoon systems on the island of Samsø. Samsø first became an island in the mid-Atlantic period, when the post-glacial sea-level rise resulted in the inundation of the paraglacial landscapes of central Denmark. Waves, currents and tides began to erode the unconsolidated Pleistocene deposits, which initiated (amongst other processes) the formation of coastal barriers and marine lagoonal sedimentation. The ongoing isostatic uplift however caused a gradual drop of relative sea-level resulting in shoreline accretion and lagoonal infilling. High-resolution geodata (LiDAR elevation model, orthophotos) and field observations facilitated the structured analysis of the island’s surface morphology and spatial reconstruction of paleo-shoreline positions. Further, a number of 31 cores were retrieved from modern and relict lagoons on the island. Stratigraphy, grain-size distribution, fossil and organic matter content were analyzed and compared. X-ray fluorescence core scanning was further employed on the fine-grained (lagoonal) sections of the cores. Age control was facilitated using radiocarbon and optically stimulated luminescence dating. Our data produced a surprisingly consistent pattern for the sedimentary successions found in the lagoons. The initial transgression can be identified along with the onset of deposition of fine-grained, organic-rich lagoonal sediments. The subsequent truncation and partial erosion of the lagoon sediments can be related to a decreasing sea-level. Based on these findings, we suggest a conceptual model that allows inferring age and elevation of transgressive and regressive stages from the lagoon sediments. Indication of geomorphological developments occurring in proximity to the lagoons (barrier formation, overwashing, dune formation) is further recorded in the deposits. These data can be used to support the proposed reconstruction of Samsø’s landscape evolution, which is primarily deduced from the present morphology and sedimentary composition of the land surface. Despite the non-continuous sedimentary record, important information of Holocene sea-level fluctuations can be retrieved from the coastal lagoons. The common occurrence of similar environments distributed along gradients of isostatic uplift/subsidence (approximately +0,7 to -0,5 mm/yr) in the south-western Baltic, makes these lagoons a valuable archive for the reconstruction of Holocene sea-level and coastal evolution.