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Blue-green algae control their buoyancy depending upon the surrounding conditions. This process is essential for Cyanobacteria development and can account for their dominance in eutrophic waters in summer. In order to determine the main regulating factors of those movements, we developed a mechanistic and deterministic model, based on differential equations, that simulates the vertical migration of Microcystis sp. In Microcystis, buoyancy regulation results from the dynamics of the carbohydrate reserve metabolism during photosynthesis. These fundamental processes are modelled daily by this vertical 1-D model named Yoyo. It describes the movement of colonies with different sizes in response to variations of environmental conditions. This paper presents the model sensitivity analysis. We individually investigated the role of light and temperature upon algal migration with colonies of two different diameters. Under a daily light cycle and a temperature of 20 • C, the model described vertical migration on a 48 h rhythm in colonies with a 300-µm diameter.