In Central Europe vast wetland areas have been converted into agricultural land over the past few centuries. Long-term spatially explicit reconstructions of wetland cover changes at regional scale are rare but such information is vital for setting appropriate wetland conservation and restoration goals. In this study wetland cover change over the past 150 years was analyzed for the Canton Zurich (Switzerland) using information from historical and current topographical maps. Mapping instructions changed significantly over time, i.e., wetlands were mapped more conservatively on older maps. Therefore a technique was developed to account for changes in mapping instructions and to reconstruct a series of comparable maps spanning 1850-2000. Wetland cover dramatically decreased from 13,759 ha in 1850 (more than 8% of the total study area) to 1,233 ha in 2000 (less than 1%). Largest loss is observed for the first half of the twentieth century when more than 50% of the total wetland loss occurred. In 1850, almost all wetland patches were connected in two large networks defined by a 500 m buffer around all wetland patches to account for typical dispersal distances of wetland animals. Despite extensive wetland loss, this networks remained largely intact until 1950, but then collapsed into many medium and small networks consisting of only few wetland patches. In addition to the direct loss of wetland habitats increased habitat fragmentation is limiting metapopulation dynamics and hindering genetic exchange between populations. Amphibians and other wetland animals are particularly prone to habitat fragmentation because of their limited migration abilities. This may lead to time-delayed extinction in the future because current species occurrence might rather reflect historical than current wetland cover and habitat configuration. Future restoration efforts should focus on reestablishing connectivity between remaining smaller wetland networks.