The photophysical properties of CdSe and ZnS(CdSe) semiconductor quantum dots in nonpolar and aqueous solutions were examined with steady-state (absorption and emission) and time-resolved (time-correlated single-photon-counting) spectroscopy. The CdSe structures were prepared from a single CdSe synthesis, a portion of which were ZnS-capped, thus any differences observed in the spectral behavior between the two preparations were due to changes in the molecular shell. Quantum dots in nonpolar solvents were surrounded with a trioctylphosphine oxide (TOPO) coating from the initial synthesis solution. ZnS-capped CdSe were initially brighter than bare uncapped CdSe and had overall faster emission decays. The dynamics did not vary when the solvent was changed from hexane to dichloromethane; however, replacement of the TOPO cap by pyridine affected CdSe but not ZnS(CdSe). CdSe was then solubilized in water with mercapto-acetic acid or dihydrolipoic acid, whereas ZnS(CdSe) could be solubilized only with dihydrolipoic acid. Both solubilization agents quenched the nanocrystal emission, though with CdSe the quenching was nearly complete. Additional quenching of the remaining emission was observed when the redox-active molecule adenine was conjugated to the water-soluble CdSe but was not seen with ZnS(CdSe). The emission of aqueous CdSe could be enhanced under prolonged exposure to room light and resulted in a substantial increase of the emission lifetimes; however, the enhancement occurred concurrently with precipitation of the nanocrystals, which was possibly caused by photocatalytic destruction of the mercaptoacetic acid coating. These results are the first presented on aqueous CdSe quantum dot structures and are presented in the context of designing better, more stable biological probes.