Aqueous-processable materials are desired to produce and commercialize eco-friendly organic solar cells. Despite the achievement of developing aqueous soluble electron donor and acceptor polymers by incorporating polar side chains (SCs), the efficiency of the greenest devices is lower than that of state-of-the-art technology processed on halogenated solvents. To investigate the impact of different substituents on structural and optical properties in solution, we considered the backbone of the PTQ10 polymer with alkyl and alkoxy SCs. We simulated oligomer chains at low and high concentration conditions via classical molecular dynamics simulations, considering both a water/ethanol mixture and chloroform as solvents. Combining an unsupervised machine learning technique and density functional theory calculations, we validated the system size for quantum calculations and investigated the impact of SCs on the excited states. Then, following the sequential QM/MM approach, we determined the absorption spectra of each polymer. From the simulations at high concentrations, we observed the stacking of different oligomers, suggesting that polymer chains already showed aggregation in solution. This is consistent with our experimental findings, as we measured a red shift of the PTQ(8bO2) spectrum when changing from a chloroform mixture to an aqueous mixture. Finally, we investigated idealized dimer interface models, whose presence of electron-donating and electron-accepting groups results in mixed signatures in the absorption spectra, widening our understanding of polymer aggregation.