For a massive scalar field with a general curvature coupling parameter, we investigate the finite temperature contributions to the Hadamard function and to the charge and current densities in the geometry of a magnetic flux carrying generalized cosmic string embedded in ($D+1$)-dimensional locally AdS spacetime with a compactified spatial dimension. For $D=4$, the geometry on the AdS boundary, in the context of the AdS/CFT duality, corresponds to a cosmic string as a linear defect, compactified along its axis. In contrast to the case of the Minkowski bulk, the upper bound on the chemical potential does not depend on the field mass and is completely determined by the length of compact dimension and by the enclosed magnetic flux. The only nonzero components correspond to the charge density, to the azimuthal current, and to the current along the compact dimension. They are periodic functions of magnetic fluxes with the period equal to the flux quantum. The charge density is an odd function and the currents are even functions of the chemical potential. At high temperatures the influence of the gravitational field and topology on the charge density is subdominant and the leading term in the corresponding expansion coincides with that for the charge density in the Minkowski spacetime. The current densities are topology-induced quantities and their behavior at high temperatures is completely different with the linear dependence on the temperature. At small temperatures and for chemical potentials smaller than the critical value, the thermal expectation values are exponentially suppressed for both massive and massless fields.