Polymethine dyes in dilute solutions show many of the electronic and optical properties required for all-optical switching applications. However, in the form of thin films, their aggregation and interactions with counterions do generally strongly limit their utility. Here, we present a theoretical approach combining molecular-dynamics simulations and quantum-chemical calculations to describe the bulk molecular packing of streptocyanines (taken as representative of simple polymethines) with counterions of different hardness (Cl and BPh4 ) and understand the impact on the optical properties. The accuracy of the force field we use is verified by reproducing experimental crystal parameters as well as the configurations of polymethine/counterion complexes obtained from electronic-structure calculations. The aggregation characteristics can be understood in terms of both polymethinecounterion and polymethinepolymethine interactions. The counterions are found to localize near one end of the streptocyanine backbones, and the streptocyanines form a broad range of aggregates with significant electronic couplings between neighboring molecules. As a consequence, the linear and nonlinear optical properties are substantially modified in the bulk. By providing an understanding of the relationship between the molecular interactions and the bulk optical properties, our results point to a clear strategy for designing polymethine and counterion molecular structures and optimizing the materials properties for all-optical switching applications.