A series of six hybrid polymers based on the mixed-valent {ε-PMoV8MoVI4O40Zn4} (εZn) Keggin unit have been synthesized under hydrothermal conditions using tritopic (1,3,5-benzenetricarboxylate (trim) or 1,3,5-benzenetribenzoate (BTB)) or ditopic (4,4′-biphenyldicarboxylate (biphen)) linkers and [M(bpy)3]2+ (M = Co, Ru) complexes as charge-compensating cations. (TBA)2[Co(C10H8N2)3][PMo12O37(OH)3Zn4](C27H15O6)4/3·1.5C27H18O6·24H2O (Co-ε(BTB)4/3) has a three-dimensional (3D) framework with two interpenetrated networks and is isostructural to (TBA)4[PMo12O37(OH)3Zn4](C27H15O6)4/3·1.5C27H18O6·8H2O (ε(BTB)4/3). In Co-ε(BTB)4/3, two tetrabutylammonium (TBA+) cations over the four present in ε(BTB)4/3 are replaced by one [Co(bpy)3]2+ complex. [Co(C10H8N2)3][PMo12O37(OH)3Zn4](C9H3O6)Co(C10H8N2)4(H2O)·16H2O (Co-ε(trim) (bpy)2) is a 1D coordination polymer with two types of CoII-containing complexes, one covalently attached to the 1D chains and the other located in the voids as the counterion. [Ru(C10H8N2)3]4[PMo12O38(OH)2Zn4]2(C9H3O6)2·42H2O (Ru-ε2(trim)2) and [Ru(C10H8N2)3]3[PMo12O37(OH)3Zn4Cl]2(C14H8O4)2·24H2O (Ru-ε2(biphen)2) contain dimeric (εZn)2 units linked by dicarboxylate linkers, and both have [Ru(bpy)3]2+ countercations. Ru-ε2(trim)2 has a 3D framework, while Ru-ε2(biphen)2 is only 2D because of the presence of chloride ions on one-fourth of the ZnII ions. [P(C6H5)4]6[PMo12O37(OH)3Zn4]2(C9H3O6)2·18H2O (PPh4-ε2(trim)2) is isostructural to Ru-ε2(trim)2. These insoluble compounds entrapped in carbon-paste electrodes exhibit electrocatalytic activity for the hydrogen evolution reaction. The effects of their structure and the nature of the counterions on the activity have been studied. For the first time, different POM-based coordination polymers are compared for catalytic H2 production using controlled-potential electrolysis. This study shows that the nature of the countercation has a strong effect on the electrocatalytic activity of the compound.