A large amount of plastic waste released into natural waters and their demonstrated toxicity have made the transformation of microplastics (MPs; < 5 mm) and nanoplastics (NPs; < 100 nm) an emerging environmental concern. Aggregation is one of the most important environmental behaviors of MPs, especially in aquatic environments, which determines the mobility, distribution and bioavailability of MPs. In this paper, the sources and inputs of MPs in aquatic environments were first summarized followed by the analytical methods for investigating MP aggregation, including the sampling, visualization, and quantification procedures of MP’ particle sizes. We critically evaluated the sampling methods that still remains a methodological gap. Identification and quantification of MPs were mostly carried out by visual, spectroscopic and spectrometric techniques, and modeling analysis. Important factors affecting MP aggregation in natural waters and environmental implications of the aggregation process were also reviewed. Finally, recommendations for future research were discussed, including (1) conducting more field studies; (2) using MPs in laboratory works representing those in the environment; and (3) standardizing methods of identification and quantification. The review gives a comprehensive overview of current knowledge for MP aggregation in natural waters, identifies knowledge gaps, and provides suggestions for future research.