Central and Eastern Europe is a region that is expected to need more data on the concentrations of persistent organic pollutants (POPs) in the ambient air in the future. Passive air sampling is a cheap screening method for comparison of contamination on various sites or for verification of information obtained by active samplers. Passive air samplers are sensitive enough to mirror even small-scale differences, which makes them capable of monitoring spatial, seasonal, and temporal variations. Different passive air samplers were employed between 1990 and 2013 from time to time in six Estonian air monitoring stations. The concentrations of PCB and its congeners, HCB, PeCB, HCH, and DDT (the same for PBDE, PCN, PCDD/F) in Estonian ambient air were very low, but they allow tracking transboundary air pollution. The main aim of this article is analysis of changes in the ambient air pollution in Estonia during a long period of time (1990–2013). Also, selection of Lahemaa background station for monitoring POPs in the European area is addressed.