Massive accumulation of plastic particles has been reported for marine ecosystems around the world, posing a risk to the biota. Freshwater ecosystems have received less attention despite most plastic litter being produced onshore and introduced into marine environments by rivers. Some studies not only report the presence of microplastics in freshwater ecosystems, but show that contamination is as severe as in the oceans. In continental waters, microplastics have been observed in both sediments (predominantly lake shores but also riverbanks) and water samples (predominantly surface water of lakes and rivers). This review highlights recent findings and discusses open questions, focussing on the methodology of assessing this contaminant in freshwater ecosystems. In this context, method harmonisation is needed in order to obtain comparable data from different environmental compartments and sites. This includes sampling strategies (at spatial and temporal scales), sample treatment (taking into consideration high levels of organic matter and suspended solids) and reliable analytical methods to identify microplastics.