Baltic coastal meadows are among the most threatened habitats in Europe, with most residual habitat being in Estonia and Sweden. We quantitatively related the changes in this habitat type in Estonia to the history of a key inhabitant — the natterjack toad (Bufo calamita Laur.). Between the 1930s and 2000s, 67% of 52 local populations of the toad disappeared; in coastal meadows, the decline was 91%. Since the 1980s, coastal grasslands have lost their value as the main habitat for the species, and occupation of secondary habitats has not balanced the disappearance of primary habitat. According to aerial photographs from 1950–51, 1970–71, and 1996–2000, 60%–83% of the coastal meadow habitats in Estonia were lost by 2000, and the toad became extinct in more than 80% of its historical habitat. The survival of local populations was related to the sizes of managed meadows and sandy areas — larger initial areas were related to better survival, probably due to larger population size. Extinction rates exceeded habitat loss rates during advanced stages of habitat loss after 1970, probably due to the additive effects of habitat fragmentation and the disappearance of critical habitat components. Hence, habitat restoration for natterjack toads should focus on large meadow areas, and should be initiated prior to advance habitat loss. Currently, however, meadow populations of the toad in Estonia are unlikely to persist without artificial re-establishment of populations.