The interaction between a fluid and a solid surface in relative motion represents a dynamical process that is central to the problem of laminar-to-turbulent transition (and consequent drag increase) for air, sea and land vehicles, as well as long-range pipelines. This problem may in principle be alleviated via a control stimulus designed to impede the generation and growth of instabilities inherent in the flow. Here, we show that phonon motion underneath a surface may be tuned to passively generate a spatio-temporal elastic deformation profile at the surface that counters these instabilities. We theoretically demonstrate this phenomenon and the underlying mechanism of frequency-dependent destructive interference of the unstable flow waves. The converse process of flow destabilization is illustrated as well. This approach provides a condensed-matter physics treatment to fluid-structure interaction and a new paradigm for flow control.