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Cobalt polypyridyl complexes efficiently catalyze hydrogen evolution in aqueous media and exhibit high stability under reducing conditions. Their stability and activity can be tuned through electronic and steric considerations, but the rationalization of these effects requires detailed mechanistic understanding. As an example, tetradentate ligands with two non-permanently occupied coordination sites show higher activity with these sites in cis compared to trans configuration. Here reaction mechanisms of the Co-polypyridyl complex [CoII(bpma)Cl2] (bpma = bipyridinylmethyl-pyridinylmethyl-methyl-amine) have been studied using hybrid density-functional theory. This complex has two exchangeable cis sites, and provides a flexible ligand environment with both pyridyl and amine coordination. Two main pathways with low barriers are found. One pathway, which includes both open sites, is hydrogen evolution from a CoII-H intermediate with a water ligand as the proton donor. In the second pathway H–H bond formation occurs between the hydride and the protonated bpma ligand, with one open site acting as a spectator. The two pathways have similar barriers at higher pH, while the latter becomes more dominant at lower pH. The calculations consider a large number of interconnected variables; protonation sites, isomers, spin multiplicities, and the identities of the open binding sites, as well as their combinations, thus exploring many simultaneous dimensions within each pathway. The results highlight the effects of having two open cis-coordination sites and how their relative binding affinities change during the reaction pathway. They also illustrate why CoII-H intermediates are more active than CoIII-H ones, and why pyridyl protonation gives lower reaction barriers than amine protonation.