Gravitational wave observations of the near-horizon region of black holes lend insight into the quantum nature of gravity. In particular, gravitational wave echoes have been identified as a potential signature of quantum gravity-inspired structure near the horizon. In this paper, we connect such observables to the language of black hole microstates in string theory and holography. To that end, we propose a toy model describing the AdS$_3$ near-horizon region of five-dimensional black holes, inspired by earlier work of Solodukhin. This model captures key features of recently constructed microstate geometries, and allows us to make three observations. First, we relate the language of AdS/CFT, in particular the holographic retarded two-point correlator, to effective parameters modeling the structure that are used in flat space gravitational wave literature. Second, we find that for a typical microstate, the `cap' of the microstructure is exponentially close to the horizon, making it an effective sub-Planckian correction to the black hole geometry, although the microstate geometry itself is classical. Third, using a microcanonical ensemble average over geometries, we find support for the claim that the gravitational wave echo amplitude in a typical quantum microstate of the black hole is exponentially suppressed by the black hole entropy.