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Nitrogen and sulphur deposition is considered as a negative factor for biodiversity, usually leading to changes in species composition and structure of plant communities, and ultimately to the impoverishment of biodiversity. In this study we investigated the variation over time (2001, 2006, 2011) in species composition and structure of the understory vegetation at varying levels of sulphur and nitrogen deposition in two conifer plantations (>100 year-old) growing in different climate areas of Poland (Scots pine at the Slowinki National Park, northern seaside; Norway spruce at the Tatrzanski National Park, southern mountains). The structure of the floor vegetation at both sites changed markedly during the studied decade, as clearly confirmed by principal component analysis. Among the environmental variables analyzed (NH4+, NO3-, SO42-, pH in the throughfall and in soil solution sampled at two different depths), only nitrates were non-significantly correlated with PC axes. The results confirmed the negative effects of the concentration of both elements on undergrowth and tree recruitment in the coastal stand (Empetro nigri-Pinetum). On the other hand, in the mountain stand (Abieti-Piceetum) we observed an increase over time of nitrophilous species typical of the beech forest, which represent the natural vegetation of this area, suggesting a gradual natural restoration of the native vegetation in the long run.