Anchored molecular catalysts provide a good step towards bridging the gap between homogeneous and heterogeneous catalysis. However, applications in an aqueous environment pose a serious challenge to anchoring groups in terms of stability. Ultrathin overlayers embedding these catalysts on the surface using atomic layer deposition (ALD) are an elegant solution to tackle the anchoring group instability. The propensity of ALD precursors to react with water leads to the question whether molecules containing aqua ligands, such as most water oxidation complexes, can be protected without side reactions and deactivation during the deposition process. We synthesized two iridium and two ruthenium-based water oxidation catalysts, which contained an aqua ligand (Ir–OH2 and Ru–OH2) or a chloride (Ir–Cl and Ru–Cl) that served as a protecting group for the former. Using a ligand exchange reaction on the anchored and partially embedded Ru–Cl, the optimal overlayer thickness was determined to be 1.6 nm. An electrochemical test of the protected catalysts on meso-ITO showed different behaviors for the Ru and the Ir catalysts. The former showed no onset difference between protected and non-protected versions, but limited stability. Ir–Cl displayed excellent stability, whilst the unprotected catalyst Ir–OH2 showed a later initial onset. Self-regeneration of the catalytic activity of Ir–OH2 under operating conditions was observed. We propose chloride ligands as generally applicable protecting groups for catalysts that are to be stabilized on surfaces using ALD.