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Climate change is leading to an increase in severity, frequency, and distribution of harmful algal blooms across the globe. For many harmful algae species in eutrophic lakes, the formation of such blooms is controlled by three factors: the lake hydrodynamics, the vertical motility of the algae organisms, and the ability of the organisms to form colonies. Here, using the common cyanobacteriumMicrocystis aeruginosaas an example, we develop a model that accounts for both vertical transport and colony dynamics. At the core of this treatment is a model for aggregation. For this, we used Smoluchowski dynamics containing parameters related to Brownian motion, turbulent shear, differential setting, and cell‐to‐cell adhesion. To arrive at a complete description of bloom formation, we place the Smoluchowski treatment as a reaction term in a set of one‐dimensional advection‐diffusion equations, which account for the vertical motion of the algal cells through molecular and turbulent diffusion and self‐regulating buoyant motion. Results indicate that Smoluchowski aggregation qualitatively describes the colony dynamics ofM. aeruginosa. Further, the model demonstrates wind‐induced mixing is the dominant aggregation process, and the rate of aggregation is inversely proportional to algal concentration. Because blooms ofMicrocystistypically consist of large colonies, both of these findings have direct consequences to harmful algal bloom formation. While the theoretical framework outlined in this manuscript was derived forM. aeruginosa, both motility and colony formation are common among bloom‐forming algae. As such, this coupling of vertical transport and colony dynamics is a useful step for improving forecasts of surface harmful algal blooms.