Structural and thermoelectric properties are reported for a specially designed class of A-site substituted perovskite titanates, (Sr1-x-yCaxNdy)TiO3. Two series of charge doped compounds (y = 0 – 0.2) were synthesized with various A-site Sr-rich or Ca-rich (Sr-poor) concentrations to have a nominally constant tolerance factor at room temperature; i.e., to have the same magnitude of the structural distortion from the cubic SrTiO3 parent material. These compounds are thus different from typically investigated (Sr1-yRy)TiO3 (R3+ = Rare Earths) where the charge doping (band filling) is convoluted with the structural changes affecting the degeneracy of the band structure. Materials were investigated using high resolution neutron powder diffraction as a function of temperature and Nd doping. We determine the room temperature structures as tetragonal I4/mcm and orthorhombic Pbnm for the Sr-rich and Ca-rich series, respectively. Three low temperature orthorhombic structures, Pbnm, Ibmm and Pbcm were also observed for the Sr-rich series; whereas, the symmetry of the Ca-rich series remains unchanged throughout the full measured temperature range. Thermoelectric properties of (Sr1-x-yCaxNdy)TiO3 were investigated and correlated with the structural variables. We succeeded in achieving a relatively high figure of merit ZT=0.07 at ~400 K in the Sr-rich Sr0.76Ca0.16Nd0.08TiO3 composition which is comparable to that of the best n-type transition metal substituted SrTi0.80Nb0.20O3 oxide material reported to date. For a fixed tolerance factor, the Nd doping enhances the carrier density and effective mass at the expense of the Seebeck coefficient. Thermal conductivity greatly reduces upon Nd doping in the Ca-rich series. With an enhanced Seebeck coefficient at elevated temperatures and reduced thermal conductivity, we predict that Sr0.76Ca0.16Nd0.08TiO3 and similar compositions have the potential to become some of the best materials in their class of thermoelectric oxides.