In modern agriculture, pesticides have been used in large quantities for controlling pests and weeds, and thus greatly improve food production. However, intensive use of common pesticides can lead to the toxicity to soils, vegetables and contamination to aqueous systems (Guo et al., 2009). In Estonia, at the beginning of the 1940s, land was taken from private owners and large collective farms were established, followed by fifty years of very intensive agricultural practice with high inputs of mineral fertilizers and agrochemicals (Truu et al., 2008). Pesticides reaching different ecosystems may alter structure and function of microbial communities (Laabs et al., 2007; Qiu et al., 2009; Lerch et al., 2009; Pesce et al., 2010). The important question of how to construct a wetland which has an efficient nitrogen removal even during pesticide exposure is to be answered. To address these issues a thorough investigation of the bacterial community and its role in wetland function has to be conducted. We have to understand this relationship between bacterial structure and function and what different factors might have an effect on the relationship. Bacterial communities is a fundamental component to study, because bacteria catalyses all ecosystem functions which are sustaining life on earth (Torsvik et al., 2002), including nitrogen cycling in terrestrial and aquatic environments. Studies linking macrophytes community composition and bacterial community composition are scarce. In addition, we are interested in the effects of different pesticides, both direct and indirect on the bacterial community structure and function. The knowledge obtained could be applied when constructing wetlands to enhance wetland function. The real-PCR analysis and the pyrosequenation technique allow better understanding on the structure and functions of microbial communities in pesticide-influenced constructed wetland ecosystems.