Freshwater ecosystems host disproportionately high biodiversity and provide unique ecosystem services, yet they are being degraded at an alarming rate. Fires, which are becoming increasingly frequent and intense due to global change, can affect these ecosystems in many ways, but this relationship is not fully understood. We conducted a systematic review to characterize the literature on the effects of fires on stream ecosystems and found that (1) abiotic indicators were more commonly investigated than biotic ones, (2) most previous research was conducted in North America and in the temperate evergreen forest biome, (3) following a control-impact (CI) or before-after (BA) design, (4) predominantly assessing wildfires as opposed to prescribed fires, (5) in small headwater streams, and (6) with a focus on structural and not functional biological indicators. After quantitatively analyzing previous research, we detected great variability in responses, with increases, decreases, and no changes being reported for most indicators (e.g., macroinvertebrate richness, fish density, algal biomass, and leaf decomposition). We shed light on these seemingly contradicting results by showing that the presence of extreme hydrological post-fire events, the time lag between fire and sampling, and whether the riparian forest burned or not influenced the outcome of previous research. Results suggest that although wildfires and the following hydrological events can have dramatic impacts in the short term, most biological endpoints recover within 5–10 years, and that detrimental effects are minimal in the case of prescribed fires. We also detected that no effects were more often reported by BACI studies than by CI or BA studies, raising the question of whether this research field may be biased by the inherent limitations of CI and BA designs. Finally, we make recommendations to help advance this field of research and guide future integrated fire management that includes the protection of freshwater ecosystems.