We consider sampled-data observer for PDE system governed by the Navier-Stokes equation on the rectangular domain. The system is exponentially stable. We aim to design an observer that exponentially converges to solution with a higher decay rate. We suggested to divide the rectangular domain into N square subdomains, where sensors provide spatially averaged discrete-time state measurements. We derive sufficient conditions ensuring regional exponential stability of the closed-loop system in terms of Linear Matrix Inequalities (LMIs) by using Lyapunov-Krasovskii method. The efficiency of the results is demonstrated by a numerical example.