Lake Pavin presents the particular feature to be meromictic: the bottom compartment of the lake exhibits a very low mixing rate with the rest of the water body. Using temperature and conductivity microstructure measurements from years 2006 and 2007, vertical dispersion coefficients (Kz) are calculated in the water column of Lake Pavin (Auvergne, France). Microstructure measurements confirm the overall shape of Kz distribution in the water column in comparison with Kz calculated from mean stratification state for the purpose of previous modelling works. Nevertheless, this study highlights the strong variability of "measured" vertical dispersion coefficient (Kz) in Lake Pavin. In fact, dissipation rates are highly intermittent in time and space and calculation of vertical dispersion coefficient can vary from 1 to 2 orders of magnitude depending on the calculation method. This study compares Kz and dissipation values from different calculation methods. At last, this study addresses the question of the impact of this variability on large-scale 1D water quality modelling by testing intermittency scenarios of Kz with biochemical water quality model AQUASIM. The importance of intermittency in the transport of solutes is highlighted.