Due to their high organic matter content, marine snow particles are hotspots for microbial activity. The heterogeneous composition of marine snow makes microbial dynamics and microbe-substrate interactions hard to examine using standard filtration and microscopy. As spatial information is crucial to better understand these interactions, we have developed cryosectioning of frozen embedded marine snow as new tool for high-resolution 3D visualization of individual aggregates. We used this method on in situ collected marine snow to conduct a series of incubations where we compared the colonization potential of a) motile Marinobacter adhaerens and their aflagellate mutants and b) bacteria extracted from two different water depths. Surprisingly, we observed attachment and penetration for M. adhaerens with and without flagella, suggesting that bacterial motility is not the only controlling factor for aggregate colonization. Our method and findings shed new light on the role of special adaptations of aggregate-associated microorganisms and pave the way for future research on specialized microbe-substrate interactions and sequential degradation of organic compounds.