The absorption and fluorescence of indole and n-cyanoindole derivatives are modeled in the gas phase and aqueous solution using high-level quantum mechanical methods and implicit solvation. These molecules have been experimentally examined as fluorescent probes for studying the structure, function, and hydration status of proteins and it is found that substitution of the cyano group on different positions of indole has diverse effects on the absorption and fluorescence spectra in water solvent. Our calculations predict that in absorption the L-b excited state is lower in energy than the L-a state for all positional isomers in the gas phase and in solution. In fluorescence, however, water solvent causes level inversion leading to emission from the L-a excited state for indole and n-cyanoindole derivatives with the cyano on the six-membered ring. However, when cyano substitution is on the five-membered ring, L-a is not stabilized enough and emission occurs from the L-b excited state. In addition, we predict that the relatively high fluorescence intensity of 4-cyanoindole in aqueous solution results from minimization of radiationless decay pathways since both absorption and fluorescence occur from the lowest excited state (unlike the other derivatives).