We have carried out time resolved stroboscopic diffraction experiments on standing surface acoustic waves (SAWs) of Rayleigh type on a LiNbO₃ substrate. A novel timing system has been developed and commissioned at the storage ring Petra Ⅲ of DESY, allowing for phase locked stroboscopic diffraction experiments applicable to a broad range of timescales and experimental conditions. The combination of atomic structural resolution with temporal resolution on the picosecond time scale allows for the observation of the atomistic displacements for each time (or phase) point within the SAW period. A seamless transition between dynamical and kinematic scattering regimes as a function of the instantaneous surface amplitude induced by the standing SAW is observed. The interpretation and control of the experiment, in particular disentangling the diffraction effects (kinematic to dynamical diffraction regime) from possible non-linear surface effects is unambiguously enabled by the precise control of phase between the standing SAW and the synchrotron bunches. The example illustrates the great flexibility and universality of the presented timing system, opening up new opportunities for a broad range of time resolved experiments.