We analyze possible effects of the dark matter environment on the atomic clock stability measurements. The dark matter is assumed to exist in a form of waves of ultralight scalar fields or in a form of topological defects (monopoles and strings). We identify dark matter signal signatures in clock Allan deviation plots that can be used to constrain the dark matter coupling to the Standard Model fields. The existing data on the Al+/Hg+ clock comparison are used to put new limits on the dilaton dark matter in the region of masses m > 10^{-15} eV. We also estimate the sensitivities of future atomic clock experiments in space, including the cesium microwave and strontium optical clocks aboard the International Space Station, as well as a potential nuclear clock. These experiments are expected to put new limits on the topological dark matter in the range of masses 10^{-10} eV < m < 10^{-6} eV.