The influence of the temporal changes in lateral inflow rate on the discharge variability in stream channels is explored through the analysis of the diffusion wave equation (i.e. the linearized Saint-Venant equation). To account for variability and uncertainty, the lateral inflow rate is regarded as a temporal random function. On the basis of the spectral representation theory, analytical expressions for the covariance function and evolutionary power spectral density of the random discharge perturbation process are derived to quantify variability in stream flow discharge induced by the temporal changes in lateral inflow rate. The treatment of the discharge variance (square root of the variance) gives us a quantitative estimate of uncertainty in predictions from the deterministic model. It is found that the discharge variability of stream flow is very large in the downstream reach, indicating large uncertainty anticipated from the use of the deterministic model. A larger temporal correlation scale of inflow rate fluctuations, representing more temporal consistency of fluctuations in inflow rate around the mean, introduces a higher variability in stream flow discharge.