The Polish breeding population (3,200–3,250 males) of the globally threatened Aquatic Warbler Acrocephalus paludicola represents almost 25% of the global population. Except for the relatively stable large population in the Biebrza valley in north-east Poland less is known about population trends of peripheral populations in western, central and south-eastern regions of the country and whether trends differ depending on region. We investigated the long-term population dynamics in 38 small populations between 1969–2013 in the four Polish regions. Summarizing the trends of all small populations of Aquatic Warblers showed a significant decline in total number of individuals and declining number of populations over time. However, population trends were distinctly different in the different regions, with stable dynamics in south-east, moderate decline in north-east and sharp decline in the central and western regions. During the study period 19 out of 38 populations became extinct (11 populations in the western region, two in central region, four in north-east region and none in the south-east region). Five of these populations were later recolonised thus suggesting a pattern of metapopulation dynamics. To mitigate the negative trends and increased risk of local and regional extinction in the western and central parts of Poland effort should be put to increasing dispersal among populations by increasing the number of stepping stone patches between the viable large eastern populations and the smaller central and western ones.