Many current quantum optical systems, such as microcavities, interact with thermal light through a small number of widely separated modes. Previous theories for photon number fluctuations of thermal light have been primarily limited to special cases that are appropriate for large volumes or distances, such as single modes, many modes, or modes of uniform spectral distribution. Herein, a theory for the general case of spectrally dependent photon number fluctuations is developed for thermal light. The error in variance of prior art is quantitatively derived for an example cavity in the case where photon counting noise dominates. A method to reduce the spectral impact of this variance is described.