Pulsed hot-electron microwave noise measurements of the (Be)MgZnO/ZnO heterostructures are presented in this work. The heterostructures of different barrier thicknesses and different bulk electron densities in ZnO layer are compared. Capacitance–voltage (C–V) measurements reveal the decrease in the two-dimensional electron gas (2DEG) peak in electron density profile at the Zn-polar BeMgZnO/ZnO interface as the BeMgZnO barrier layer thickness decreases. For thin-barrier heterostructures, the peak disappears and only the bulk electron density is resolved in C–V measurements. The excess noise temperature at ∼10 GHz in thick-barrier heterostructures is noticeably higher (∼10 times) compared to thin-barrier heterostructures, which is attributed to the strong noise source in the contacts of the former. In the case of thin-barrier heterostructures, at electric fields above ∼10 kV/cm and electron density ≳1×1017cm−3, strong noise source is resolved, which was also observed earlier in the Ga-doped ZnO films due to the formation of self-supporting high-field domains. However, for the low electron densities (≲6 ×1016 cm−3), the aforementioned noise source is not observed, which suggests the importance of a deep ZnO/GaN interface with 2DEG for power dissipation. The hot-electron temperature dependence on the dissipated power of those low-electron-density heterostructures is similar to that of O-polar ZnO/MgZnO. The estimated electron energy relaxation time in ZnO/MgZnO is ∼0.45 ps ± 0.05 ps at dissipated electrical power per electron of ∼0.1 nW/el and approaches ∼0.1 ps as the dissipated power is increased above ∼10 nW/el.