The first countrywide survey of bird fauna of the mires in Estonia was already carried out during 1948-1957. Regular re-inventories were started in 1968. The interval between baseline (1940s-1950s) and the first re-survey varied from 15 to 30 years and the interval between successive re-surveys between 1 to 20 years. Altogether, we used data from surveys in 60 survey areas, covering totally 71 260 ha (22 % of total area of peatlands which are in near-natural state nowadays). Surveyed mire-patches varied from 162 to 6180 ha depending from the size of mire. Mire patches are surveyed using single-visit transect counts. Large mire-patches are surveyed with several single-visit transects, covering the total area of the mire patch. We had sufficient data for reconstruction of population trends for 11 wader species breeding in mires of Estonia. The trends for the wader populations were modeled using generalized additive mixed model (GAMM) with mire-patch as random intercept. To deal with heterogeneity, models with no weighting, patch-area weighting and maximum population size weighting were analyzed. The curves of the fixed part of the unweighted trend model seemed to be affected from several mire-patches, that have high-resolution temporal data or either were possibly biased by the high number of very small mire-patches, having low abundance. However, taking the size of mire-patch into account (area-weighted models) gave reasonable results that should represent the long-term population trends of mire-breeding waders.