The destruction of wetlands due to afforestation areas is a common activity in temperate and subtropical regions in Southern America. The expansion of pine (Pinus elliottii Engelm.) in the Coastal Plain of Southern Brazil is critical and its impacts on aquatic biodiversity are little known. We tested the hypotheses that: (1) pine occurrence diminishes the macrophyte richness and changes the macrophyte composition in ponds; (2) beta-diversity between natural and pine ponds is determined mainly by species nestedness (species loss). Sampling was carried out from 2007 to 2009 in five ponds in pine invasion matrix and five ponds in native grassland matrix. In natural ponds, the total richness was 87 species, followed by 51 species in pine ponds. From the total richness, 42 species were shared between natural and pine ponds. The natural ponds were richer than the pine ponds along the entire study, and the composition of macrophyte species was different between natural and pine ponds. Comparing natural ponds with each other and pine ponds with each other, the species turnover (species replacement) was determinant for beta-diversity, however, when we compared natural and pine ponds, we found that nestedness and species turnover were equivalent for beta-diversity. The increase in the nestedness mechanism indicates that the pine occurrence implies in species loss in Southern Brazil ponds. The change of hydroperiod may be one of the causes for the macrophyte species loss. The removal of pine from areas destined to conservation in Southern Brazil is urgent as well as a proper management of pine plantations in order to minimise its expansions and impacts in the aquatic biodiversity, since 90% of its wetlands have been already lost.