We consider the dephasing of two internal states |0> and |1> of a trapped impurity atom, a so-called atomic quantum dot (AQD), where only state |1> couples to a Bose-Einstein condensate (BEC). A direct relation between the dephasing of the internal states of the AQD and the temporal phase fluctuations of the BEC is established. Based on this relation we suggest a scheme to probe BEC phase fluctuations nondestructively via dephasing measurements of the AQD. In particular, the scheme allows to trace the dependence of the phase fluctuations on the trapping geometry of the BEC.