The wetlands found in the Brazilian Cerrado are poorly studied environments regarding ecological aspects. Assessing the diversity of aquatic invertebrates in wetlands is a challenging task, since there are no standard sampling methods that minimize the spatial effects caused by macrophytes. The aim of this study was to evaluate the efficiency of a new sampling method for assessing Cladocera richness in macrophyte-rich wetlands of Brazilian Cerrado. In six wetlands, one transect was established which corresponded to a gradient of depth or change in aquatic vegetation. Samples containing cladocerans were collected using plankton net dragged among aquatic vegetation in the dry and rainy seasons. The species accumulation curves using non-parametric estimators and the overestimation of richness were used to determine the sampling efficiency. The species accumulation curves showed different asymptotic trends regarding the season and wetland studied. Especially in the rainy season, an asymptotic trend was not observed in two of the wetlands studied, which may reflect the influence of seasonality on Cladocera assemblage. Nevertheless, the overestimation of species richness showed that the method of sampling was able to find more than 60% of the estimated species richness, regardless of season or wetland studied. These results indicate that the method employed for sampling Cladocera in the Cerrado wetlands can be considered adequate.