We introduce a detector that selectively probes the phononic excitations of a cold Bose gas. The detector is composed of a single impurity atom confined by a double-well potential, where the two lowest eigenstates of the impurity form an effective probe qubit that is coupled to the phonons via density-density interactions with the bosons. The system is analogous to a two-level atom coupled to photons of the radiation field. We demonstrate that tracking the evolution of the qubit populations allows probing both thermal and coherent excitations in targeted phonon modes. The targeted modes are selected in both energy and momentum by adjusting the impurity's potential. We show how to use the detector to observe coherent density waves and to measure temperatures of the Bose gas down to the nanokelvin regime. We analyze how our scheme could be realized experimentally, including the possibility of using an array of multiple impurities to achieve greater precision from a single experimental run.