The state of aggregation of compounds, especially drugs, in the cores of nanoparticles (NPs) formed by rapid precipitation is a significant unresolved issue. The state can control the dissolution kinetics from the NP, bioavailability, and chemical stability of the compound. A block-copolymer-directed rapid precipitation process is used to form ≈100 nm NPs comprising mixtures of hydrophobic species including fluorescent probe molecules. Fluorescence measurements are used to probe the state of aggregation and dynamics of rearrangement of pyrene (Py), Hostasol Yellow (HosY), and amphotericin B (AmpB) in NP cores. The Flory–Huggins theory of mixing is used to predict the miscibility or phase separation of the fluorophores from the host NP core material (polystyrene, cholesterol, or polycaprolactone). For Py, excimer fluorescence shows an initial microphase separation in the polystyrene core. Over time the Py redistributes more uniformly with a decrease in excimer and increase in monomer fluorescence. The Flory–Huggins theory predicts the miscibility. For HosY, the fluorescence quenching is not time-dependent, thus indicating stability of the microphase-separated fluorophores, which is consistent with the Flory–Huggins theory calculations. For the drug compound AmpB, the amphiphilic character of the molecule creates unusual “anti-Ostwald” ripening behavior in which the size distribution decreases and narrows over time, and the fluorescence demonstrates an increased ordering in the NP core over time—opposite to the behavior observed for Py.