The ecological state of lake ecosystems worldwide has deteriorated over the past decades. Eutrophication and climate change contribute to the increase of algal blooms, in particular of toxic cyanobacteria blooms, which currently constitute a main concern in the management of water resources. Modelling tools are of central importance to better understand the impact of climate change on the thermal regime of small and shallow lakes and its relation to phytoplankton growth. The recognized three-dimensional hydrodynamic model TELEMAC3D was recently coupled with the biogeochemical library Aquatic EcoDynamics (AED). Here, the coupled model is applied on Lake Champs-sur-Marne, a small and shallow lake (Great Paris), which suffers from recurrent cyanobacterial blooms.The available data set includes high-frequency data. Water temperature, oxygen, nitrate, chlorophyll and phycocyanin are measured at a 10mn time step. The results of a simulation run from February to November 2019 are presented. The model performance is assessed thoroughly against multiple variables and at different time scales. Regarding the thermal regime of this polymictic lake, the simulated water temperature is in very good agreement with observations. Moreover, the alternation of mixing and stratification is well captured by the model. The seasonal evolution of the phytoplankton biomass is correctly reproduced as well as its distribution between the main phytoplankton groups. Furthermore, the dynamics of dissolved oxygen and nitrate is well captured. This fully coupled 3D hydrodynamic-biogeochemical model provides a new robust tool for modelling the interplay between hydrodynamics and biogeochemistry in small polymictic lakes which represent the majority of global lakes.