The continuum theory of incoherently scattered electromagnetic waves is modified in order to include possible effects of thermally induced chemical fluctuations. These fluctuations are taken into account by introducing fluctuating parts in the production and loss terms of the continuity equations. An equivalent ionspheric model is developed for three types of ionized species, i.e., electrons and negative and positive ions. A matrix formulation gives simultaneous access to fluctuating parts of each charged component. Numerical results indicate that chemical fluctuations are important over the height range where negative ions are comparable or greater than the electron concentration. Strong enhancements of the incoherent scatter cross section occur for frequency shifts smaller than approximately 20 Hz. A simple approximation is given for the contribution of chemical fluctuations.