Estuaries and coastal seas are hotspots of diversity and productivity that have attracted people for settlement and resource use since earliest times. Here, we present the timelines of human-induced changes in 12 estuaries and coastal seas in Europe, North America and Australia. Using palaeontological, archaeological, historical, fisheries and ecological records, we reconstructed changes in marine species, habitats, and water quality since human occupation. Human impacts started to deplete marine resources during Roman Times in the Adriatic Sea, Medieval Times in the Baltic and North Seas, and Colonial Times in North America and Australia. The acceleration and intensification of human impacts over the last 150-300 years, however, shifted all systems to a similarly degraded state today. In general, overexploitation caused the sequential depletion, collapse, or extinction of most large consumers, with many mammals and birds reaching low levels around 1900. Fisheries impacts and land-use patterns destroyed 50-90 % of coastal wetlands, seagrass beds, oyster banks, and other seafloor habitats. Land run-off and waste water discharges exponentially increased sediment and nutrient loads since the 1800s but especially since 1950 leading to eutrophication and oxygen depletion. Furthermore, invasion rate of exotic species increased especially in the 20^th century. Today, all 12 systems are fundamentally transformed ecosystems with changed diversity, food-web structure and ecosystem functioning. Conservation efforts in the 20^th century turned some negative trends around and enabled recovery of some birds and mammals. These successes together with a good understanding of the environmental history can provide critical baselines and guide future conservation efforts.