The Metabolic Theory of Ecology (MTE) integrates first principles of thermodynamics, chemical kinetics, and physics to mathematically describe how metabolic processes are some function of body mass and temperature. The theory has had success in predicting ecological processes at multiple scales in terrestrial systems. Empirical tests of the MTE using data on secondary production in streams and whole-stream metabolism have supported the theory to a lesser degree. We found that patterns better fit MTE predictions when stream conditions most closely approximated steady state conditions. Frequent disturbance and pulsed resources, particularly in highly heterotrophic systems, are two mechanisms contributing to observed deviations from MTE predictions. These results do not necessarily indicate that the theory ought to be refuted.  Rather, resource and non-equilibrium dynamics must be incorporated within the MTE. In turn, stream data collection ought to have a greater focus on more frequent monitoring of ecological processes rather than point measures. Greater temporal resolution of data from streams will allow for better estimation of rates (and variances) over annual time scales, which is needed to further test and refine the MTE.