Summary: We discuss an approximate model for the propagation of deep irrotational water waves, specifically the model obtained by keeping only quadratic nonlinearities in the water waves system under the Zakharov/Craig-Sulem formulation. We argue that the initial-value problem associated with this system is most likely ill-posed in finite regularity spaces, and that it explains the observation of spurious amplification of high-wavenumber modes in numerical simulations that were reported in the literature. This hypothesis has already been proposed by D. M. Ambrose et al. [Proc. R. Soc. Lond., Ser. A, Math. Phys. Eng. Sci. 470, No. 2166, Article ID 20130849, 16 p. (2014; Zbl 1371.35210)] but we identify a different instability mechanism. On the basis of this analysis, we show that the system can be “rectified”. Indeed, by introducing appropriate regularizing operators, we can restore the well-posedness without sacrificing other desirable features such as a canonical Hamiltonian structure, cubic accuracy as an asymptotic model, and efficient numerical integration. This provides a first rigorous justification for the common practice of applying filters in high-order spectral methods for the numerical approximation of surface gravity waves. While our study is restricted to a quadratic model, we believe it can be generalized to any order and paves the way towards the rigorous justification of a robust and efficient strategy to approximate water waves with arbitrary accuracy. Our study is supported by detailed and reproducible numerical simulations.