Diblock copolymers of poly(isoprene-b-ethylene oxide), PI-b-PEO (IEO), are employed as templates for the development of nanostructured polymer electrolytes by salt-doping. For this purpose, lithium triflate (CF3SO3Li, LiTf) and 1-ethyl-3-methylimidazolium trifluoromethanesulfonate (CF3SO3-C6H11N2, EMITf) salts were separately introduced at various [EO]:[salt] ratios. The local structure, nanodomain morphology and ion dynamics of the resulted block copolymer electrolytes were investigated by infrared spectroscopy, X-ray scattering, differential scanning calorimetry and dielectric spectroscopy. The structural investigation revealed strong effects of both LiTf and EMITf salt addition to the copolymer nanodomain morphology. These include transitions between different ordered nanophases and an increased domain spacing. The latter was independent of the kind of salt providing the possibility of studying ion transport under identical nanodomain sizes but in the presence of different interactions. Ionic conductivity in the two systems was fundamentally different. In IEO/EMITf ionic conductivity was much higher and comparable to the PEO/EMITf case. However, in IEO/LiTf, ion conductivity was reduced by a factor of a 100 relative to the PEO/LiTf case. This reflects combined effects of increased interaction parameter and of preferential wetting of electrodes. These results suggest ways for manipulating ion transport in polymer electrolytes.