Biological aggregates play important roles in microbial life, with far-reaching implications for environmental processes, human health, and biotechnology. By assembling into collective structures, microorganisms modify their mechanical stability, access to light, oxygen and nutrients, and transport in suspension, with consequences ranging from pathogen transmission to harmful algal blooms and carbon export into the deep ocean. Understanding these systems requires unraveling the interplay between biological activity, aggregate architecture, the extracellular matrix and the surrounding flow. How do aggregates form, grow, and fragment? How do their structure, cellular metabolism, and material properties govern vertical transport and nutrient exchange? And how can insights from controlled laboratory experiments inform predictions in turbulent, heterogeneous natural environments? This mini-symposium brings together perspectives from microbiology, soft-matter physics, fluid mechanics, and environmental engineering to address these challenges. Connecting research on wastewater photogranules, cyanobacterial blooms, biofilms, ocean turbulence, and sinking marine particles, the meeting aims to identify shared physical principles and bridge scales from individual microorganisms to ecosystem-level processes.