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Macroscopic organic aggregates, which are > 500 m and known as marine and lake snow, are important components in the turnover, decomposition and sinking flux of both organic and inorganic matter and elements in aquatic ecosystems. They are composed of various organic and inorganic materials depending largely on the given system and environmental conditions. The systems include the pelagic limnetic, the neritic and oceanic marine region, as well as shallow turbid environments, e.g. rivers, the littoral zone of lakes, estuaries and tidally affected coastal areas with intense turbulence and a high load of suspended matter. Aggregate abundance and size vary greatly among these systems. Macroaggregates are heavily colonized by bacteria and other heterotrophic microbes and greatly enriched in organic and inorganic nutrients as compared to the surrounding water. During the last 15 yr, many studies have been carried out to examine various aspects of the formation of aggregates, their microbial colonization and decomposition, nutrient recycling and their significance for the sinking flux. They have been identified as hot-spots of the microbial decomposition of organic matter. Further, microaggregates, which are < 5 to 500 m in size and stained by different dyes, such as transparent exopolymer particles (TEP) and Coomassie blue-stained particles, have been discovered and shown also to be important in the formation and decomposition of macroaggregates. In this review we give an overview of the present state of the microbial ecology of macro-and microaggregates, including the mentioned points but highlighting in particular the recent findings on the bacterial colonization of aggregates using molecular tools, their microbial decomposition and mineralization, and the significance of protozoans and metazoans for the colonization and decomposition of macroaggregates. Today it is evident that not only the aggregates but also their surroundings are sites and hot-spots of microbial processes, with the plume of solutes leaking out of the aggregates and greatly extending the volume of the intense decomposition processes. This microheterogeneity has important implications for the spatial and temporal dynamics of the organic-matter field in aquatic ecosystems and for our understanding of how heterotrophic organisms are involved in the decomposition of organic matter. The significance of aggregate-associated microbial processes as key processes and also for the overall decomposition and flux of organic mattervaries greatly among the various systems, and is greatly affected by the total amount of suspended particulate matter. A conclusion from the presented studies and results is that the significance of bacteria for the formation and decomposition of aggregates appears to be much greater than previously estimated. For a better understanding of the functioning of aquatic ecosystems it is of great importance to include aggregate-associated processes in ecosystem modeling approaches.