We study the two dimensional time dependent Large Eddy Simulation method applied to the incompressible Navier-Stokes system with Smagorinsky's eddy viscosity model and a filter width that depends on the local mesh size. The discrete model is based on the implicit Euler scheme and a conforming finite element method for the time and space discretizations, respectively. We establish a reliable and efficient a posteriori error estimation between the numerical LES solution and the exact solution of the original Navier-Stokes system, which involves three types of error indicators respectively related to the filter and to the discretizations in time and space. Numerical results show the effectiveness of adaptive simulations.