The population dynamics of shrews (Soricidae) are not well known even though they form an important part of forest ecosystems and represent suitable bioindicators of ecosystem quality. The aim of this study was to evaluate the population dynamics of shrews in mountain and upland forest clearings in four study areas within the Czech Republic and to reveal how climatic factors influenced fluctuations in their abundance for a decade (2007–2017). In total, we trapped 7,538 individuals of 18 small mammal species. From 760 individuals of seven shrew species, the common shrew (Sorex araneus) was significantly dominated in all study areas. We did not observe any significant, regular multi-annual cycles of the common shrew. However, a cross-correlation in density fluctuation of this species was detected in all mountain areas indicating the influence of environmental factors acting on a larger geographical scale. The autumn abundance of shrews was dependent on the subset of climatic variables, together explaining 56% of the variance in the linear regression model. Except for the length of the snow cover of ≥ 5 cm, all other significant variables were associated with North Atlantic Oscillation (NAO). Longer duration of snow cover during the winter before trapping, higher average NAO value during months before trapping, and NAO value in September influenced negatively the autumn abundance of shrews, contrary, higher value of NAO in May and October increased the abundance. Our results demonstrate the sensitivity of shrews to winters with a longer period of snow cover and to climatic oscillations associated with the NAO, whose effect is monthly dependent and probably indirectly influencing shrews through their prey.