This contribution reports a series of anionic narrow-band-gap self-doped conjugated polyelectrolytes (CPEs) with π-conjugated cyclopenta-[2,1-b;3,4-b′]-dithiophene-alt-4,7-(2,1,3-benzothiadiazole) backbones, but with different counterions (Na+, K+, vs tetrabutylammonium) and lengths of alkyl chains (C4 vs C3). These materials were doped to provide air-stable, water-soluble conductive materials. Solid-state electrical conductivity, thermopower, and thermal conductivity were measured and compared. CPEs with smaller counterions and shorter side chains exhibit higher doping levels and form more ordered films. The smallest countercation (Na+) provides thin films with higher electrical conductivity, but a comparable thermopower, compared to those with larger counterions, thereby leading to a higher power factor. Chemical modifications of the pendant side chains do not influence out of plane thermal conductivity. These studies introduce a novel approach to understand thermoelectric performance by structural modifications.