The primordial fluctuations on large scales are adiabatic, but on smaller scales this need not be the case. Here we derive the general analytical framework to compute the stochastic gravitational wave background induced by primordial cold dark matter isocurvature fluctuations on small scales. We find that large isocurvature fluctuations can yield an observable gravitational wave signal, with a spectrum distinct from the one induced by adiabatic perturbations, and we provide for the first time the exact analytic expression of the kernel necessary to compute this signal. We then forecast the constraining power of future gravitational wave detectors on dark matter isocurvature on small scales and find they will dramatically improve on existing constraints.