Our goal in this paper is to apply a normal forms method to estimate the Sobolev norms of the solutions of the water waves equation. We construct a paradifferential change of unknown, without derivatives losses, which eliminates the part of the quadratic terms that bring non zero contributions in a Sobolev energy inequality. Our approach is purely Eulerian: we work on the Craig-Sulem-Zakharov formulation of the water waves equation. In addition to these Sobolev estimates, we also prove $L^2$-estimates for the $\partial_x^\alpha Z^\beta$-derivatives of the solutions of the water waves equation, where $Z$ is the Klainerman vector field $t\partial_t +2x\partial_x$. These estimates are used in another paper where we prove a global existence result for the water waves equation with smooth, small, and decaying at infinity Cauchy data, and we obtain an asymptotic description in physical coordinates of the solution, which shows that modified scattering holds. The proof of this global in time existence result relies on the simultaneous bootstrap of some Hölder and Sobolev a priori estimates for the action of iterated Klainerman vector fields on the solutions of the water waves equation. The present paper contains the proof of the Sobolev part of that bootstrap.