Coastal lagoons are highly productive and biologically diverse landscape features that sustain a range of valuable natural services to societies. Acting as an interface between land and sea, they evolve naturally, but are also vulnerable to various forms of human activity. Based on old cartographic material, LiDAR elevation data, Holocene sea level histories, and shoreline modelling, we study the development of coastal lagoons on the postglacially uplifting, tideless coast of the brackish water Baltic Sea. Ecological succession of habitats along the path from bays to semi-enclosed lagoons, coastal lakes or bogs is discussed utilizing community structure analysis of habitat building bottom vegetation. There are about 600 lagoons in Estonia, but they are typically small (bigger ones up to 6 km2) and mostly <1 m deep. Due to ongoing postglacial uplift (1.5−3.4 mm/a), lagoons are just a relatively short (50−500-years long) transitional phase in a long (up to ∼10 000-years) succession. Locating at an altitude of up to 20−30 m, some older, more resilient palaeolagoons can be nowadays distinguished as lakes or bogs, while smaller ones have blended into the surrounding landscape. The contemporary lagoons are ephemeral too, because the emerging terrain has already been flattened by erosion and sedimentation. After separation from the sea, the brackish water habitat is gradually replaced with freshwater habitat and both biodiversity and plants coverage usually increases. As organic deposits build up, low-growth shores are replaced with high-growth vegetation; reedbeds expand. Detached from their marine past, communities typical for lakes, fens, bogs or forests are finally formed. As a result of eutrophication, ongoing climate change and sea level rise, the balance between emergence of new lagoons and their disappearance due to distancing and swamping has shifted over the past 100 years.