Self-assembling nanoparticles of amphiphilic polymers are viable delivery vehicles for transporting hydrophobic molecules across hydrophilic media. Noncovalent contacts between the hydrophobic domains of their macromolecular components are responsible for their formation and for providing a nonpolar environment for the encapsulated guests. However, such interactions are reversible and, as a result, these supramolecular hosts can dissociate into their constituents amphiphiles to release the encapsulated cargo. Operating principles to probe the integrity of the nanocarriers and the dynamic exchange of their components are, therefore, essential to monitor the fate of these supramolecular assemblies in biological media. The co-encapsulation of complementary chromophores within their nonpolar interior offers the opportunity to assess their stability on the basis of energy transfer and fluorescence measurements. Indeed, the exchange of excitation energy between the entrapped chromophores can only occur if the nanoparticles retain their integrity to maintain donors and acceptors in close proximity. In fact, energy-transfer schemes are becoming invaluable protocols to elucidate the transport properties of these fascinating supramolecular constructs in a diversity of biological preparations and can facilitate the identification of strategies to deliver contrast agents and/or drugs to target locations in living organisms for potential diagnostic and/or therapeutic applications.