The synthesis of a new oligophenyleneethynylene (OPE)-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) bolaamphiphile 1 and its aqueous self-assembly are reported. Compound 1 forms H-type aggregates in aqueous and polar media, as demonstrated by UV/Vis and fluorescence experiments. Concentration-dependent (1)H NMR studies in CD3CN reveal that the BODIPY units are arranged on top of each other into π-stacks with H-type excitonic coupling, as supported by ROESY NMR and theoretical calculations and visualized by Cryo-SEM studies. A detailed analysis of the spectral changes observed in temperature-dependent UV/Vis studies reveals that 1 self-assembles in a non-cooperative (isodesmic) fashion in water. The hydrophobic interior of these self-assembled structures can be exploited to encapsulate hydrophobic dyes, such as tetracene and anthracene. Both dyes absorb in a complementary region of the UV/Vis spectrum and are small enough to interact with the hydrophobic segments of 1. Temperature-dependent UV/Vis studies reveal that the spectral changes associated to the encapsulation mechanism of tetracene can be fitted to a Boltzmann function, and the initially flexible fibres of 1 rigidify upon guest addition. In contrast, the co-assembly of 1 and anthracene is a highly cooperative process, which suggests that a different class of (more-ordered) aggregates is formed. TEM and Cryo SEM imaging show the formation of uniform spherical nanoparticles, indicating that a subtle change in the guest molecular structure induces a significant change in the encapsulation mechanism and, consequently, the aggregate morphology.