The abandonment of less productive agricultural land and the intensification of agricultural land use are the main features of the Common Agricultural Policy (CAP) that Croatia will enforce now as new member of the EU. Due to demographic changes and the economic transition in Croatia resulting from war in the 1990s, substantial tracts of agricultural land were abandoned. We investigated two habitat types in the protected floodplain landscape of Lonjsko polje in the continental part of the country: arable land and pastures. Both habitats were maintained by agricultural management and suffered from partial abandonment. Land abandonment increased the susceptibility to encroachment by the invasive plant species Amorpha fruticosa. Data on bird communities were obtained during the breeding season in 2010 while there were high water levels in the floodplain. Data were collected from 63 points, and a total of 1447 individuals from 70 species were recorded during the study. We found that the bird community structure was primarily related to the presence/abandonment of agricultural land use and the habitat type. Further, we detected that the bird community structure in the same habitat type differed by management intensity. Open habitat specialists were most influenced by land abandonment. However, the conservation value (according to the Species of European Conservation Concern value, SPEC) of grazed pastures and abandoned pastures did not differ significantly, in part because the overgrown pastures with high water levels were found to be suitable for Acrocephalus species. The shift in bird community structure between abandoned and managed arable lands were smaller than those detected in the pastoral communities. Because land abandonment is a widespread phenomenon in Croatia, we emphasize the urgent need for a nationwide monitoring program for farmland birds to register the resulting changes in farmland bird communities and to develop appropriate agri-environment measures to mitigate the process.