We study the passivation and recovery of shallow and deep levels in Si-doped AlGaAs exposed to CH4/H-2 and H-2 reactive ion etching (RIE). The carrier concentration depth profile is determined by capacitance-voltage measurements. The activation energy to recover the silicon donors is found to be 1.1 eV for samples exposed to CH4/H-2 RIE and 1.3 eV for samples exposed to H-2 RIE. We study the behavior of DX centers in Si-doped AlGaAs layers after RIE exposure and subsequent thermal annealing by using deep level transient spectroscopy. For CH4/H-2 RIE a new emission is detected at the high temperature side. We identify this emission as the DX3 center, which is assigned to a DX center with three aluminum atoms surrounding the Si donor. This DX center is only detected on the samples exposed to CH4/H-2 RIE. We explain the formation of this deep level to the highly selective removal of Ga atoms in favor of Al atoms. Consequently Al-rich regions are created near the surface.