Plastic pollution poses a serious risk to the oceans, freshwater ecosystems and land-based agricultural production. Most plastic waste enters rivers and then reaches the oceans, where its fragmentation process begins and the forming of microplastics (MPs) and nanoplastics (NPs). These particles increase their toxicity by the exposition to external factors and bind environmental pollutants, including toxins, heavy metals, persistent organic pollutants (POPs), halogenated hydrocarbons (HHCs) and other chemicals, which further and cumulatively increase the toxicity of these particles. A major disadvantage of many MNPs in vitro studies is that they do not use environmentally relevant microorganisms, which play a vital role in geobiochemical cycles. In addition, factors such as the polymer type, shapes and sizes of the MPs and NPs, their exposure times and concentrations must be taken into account in in vitro experiments. Last but not least, it is important to ask whether to use aged particles with bound pollutants. All these factors affect the predicted effects of these particles on living systems, which may not be realistic if they are insufficiently considered. In this article, we summarize the latest findings on MNPs in the environment and propose some recommendations for future in vitro experiments on bacteria, cyanobacteria and microalgae in water ecosystems.