The functional group-directed structures of coordination polymers (CPs) and metal–organic frameworks (MOFs) have made them key candidates for proton exchange membranes in fuel cell technologies. Sulfonate group chemistry is well established in proton conducting polymers but has seen less exploration in CPs. Here, we report solvent-directed crystal structures of Cu2+ and Ca2+ CPs constructed with naphthalenedisulfonate (NDS) and anthraquinone-1,5-disulfonate (ADS) ligands, and we correlate single crystal structures across this set with proton conductivities determined by electrochemical impedance spectroscopy. Starting from the Cu2+-based NDS and aminotriazolate MOF designated Cu-SAT and the aqueous synthesis of the known Ca2+-NDS structure incorporating water ligands, we now report a further five sulfonate CP structures. These syntheses include a direct synthesis of the primary degradation product of Cu-SAT in water, solvent-substituted Ca-NDS structures prepared using dimethylformamide and dimethylsulfoxide solvents, and ADS variants of Cu-SAT and Ca-NDS. We demonstrate a consistent 2D layer motif in the NDS CPs, while structural modifications introduced by the ADS ligand result in a 2D hydrogen bonding network with Cu2+ and aminotriazolate ligands and a 1D CP with Ca2+ in water. Proton conductivities across the set span 10−4 to >10−3 S cm−1 at 80 °C and 95% RH. These findings reveal an experimental structure–function relationship between proton conductivity and the tortuosity of the hydrogen bonding network and establish a general, cross-structure descriptor for tuning the sulfonate CP unit cell to systematically modulate proton conductivity.