Harmful blooms of the filamentous cyanobacteria Planktothrix rubescens have become common in many lakes as they have recovered from eutrophication over the last decades. These cyanobacteria, capable of regulating their vertical position, often flourish at the thermocline to form a deep chlorophyll maximum. In Lake Zurich (Switzerland), they accumulate during stratified season (May–October) as a persistent metalimnetic thin layer (~2 m wide). This study investigated the role of turbulent mixing in springtime layer formation, its persistence over the summer, and its breakdown in autumn. We characterised seasonal variation of turbulence in Lake Zurich with four surveys conducted in April, July and October of 2018 and September of 2019. Surveys included microstructure profiles and high-resolution mooring measurements. In July and October, the thin layer occurred within a strong thermocline ( N ≳ 0.05 s−1 ) and withstood significant turbulence, observed as turbulent kinetic energy dissipation rates ( ≈ 10−8 W kg−1 ). Vertical turbulent overturns –monitored by the Thorpe scale– went mostly undetected and on average fell below those estimated by the Ozmidov scale ( L O ≈ 1 cm). Consistently, vertical diffusivity was close to molecular values, indicating negligible turbulent fluxes. This reduced metalimnetic mixing explains the persistence of the thin layer, which disappears with the deepening of the surface mixed layer in autumn. Bi-weekly temperature profiles in 2018 and a nighttime microstructure sampling in September 2019 showed that nighttime convection serves as the main mechanism driving the breakdown of the cyanobacterial layer in autumn. These results highlight the importance of light winds and convective mixing in the seasonal cycling of P. rubescens communities within a strongly stratified medium-sized lake.