The episodic hyperproduction of mucilage macroaggregates in the northern Adriatic Sea creates an important site for the accumulation, transformation, and degradation of organic matter. In this review, the structure and function of macroaggregate components in relation to their macrogel and colloidal fractions are discussed. High resolution electron microscopy showed a very complex structure, a honeycomb-like structure of the mucus macroagregates that might grow to macroscopic sizes. The process of the formation and microbial interaction with the physicochemical diversity of the organic matter pool is poorly understood. Whether the in situ bacteria react to the carbohydrate-rich mucus as an imbalance in its C:N:P ratio or whether the mucus is in fact largely a bacterial construct in relation to high dissolved organic carbon levels is unknown. The majority of carbohydrate and protein macroaggregate pools are potentially degradable, while the great majority of lipids can be preserved in the water column and exported away or finally deposited on the seabed. Our present knowledge indicates that different macroaggregate fractions and components are subjected to compositional selective reactivity, with important implications for macroaggregate persistence. Future work should reconcile the discrepancies between bacterial ectoenzyme potential activities and biogeochemical degradation sequences based on actual measurements. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies, has profound implications for the function of these complex communities. We need to improve our understanding of the dynamic relationship among bacteria, other microorganisms, and a variety of organic matter forms.