Plastic is one of the most commonly produced and used materials in the world due to its outstanding features. However, the worldwide use of plastics and poor waste management have led to negative impacts on ecosystems. Plastic degradation in the environment leads to the generation of plastic particles with a size of <5 mm, which are defined as microplastics (MPs). These represent a global concern due to their wide dispersion in water environments and unclear potential ecotoxicological effects. Different studies have been performed with the aim of evaluating the presence and impacts of MPs in the marine environment. However, the presence of MPs in freshwater systems is still poorly investigated, making data retrieval a difficult task. The purpose of this review is to identify the main aspects concerning MPs pollution sources in lakes and rivers, with a focus on freshwater sediments as a site of accumulation and as the habitat of benthic organisms, which are key components of food webs and play a fundamental role in energy/contaminant transfer processes, but are still poorly considered. Through this review, the sources and fate of MPs in freshwater are analysed, ecotoxicological studies focused on sediments and benthic fauna are exposed, the most frequently used sampling and analysis strategies are reported, and future trends of MPs analysis in this field are proposed.