Slight changes in climate, such as the rise of temperature or alterations of precipitation and evaporation, will dramatically influence nearly all freshwater and climate-related hydrological behavior on a global scale. The hyporheic zone (HZ), where groundwater (GW) and surface waters (SW) interact, is characterized by permeable sediments, low flow velocities, and gradients of physical, chemical, and biological characteristics along the exchange flows. Hyporheic metabolism, that is biogeochemical reactions within the HZ as well as various processes that exchange substances and energy with adjoining systems, is correlated with hyporheic organisms, habitats, and the organic matter (OM) supplied from GW and SW, which will inevitably be influenced by climate-related variations. The characteristics of the HZ in acting as a transition zone and in filtering and purifying exchanged water will be lost, resulting in a weakening of the self-purification capacity of natural water bodies. Thus, as human disturbances intensify in the future, GW and SW pollution will become a greater challenge for mankind than ever before. Biogeochemical processes in the HZ may favor the release of carbon dioxide (CO2), nitrous oxide (N2O), and methane (CH4) under climate change scenarios. Future water resource management should consider the integrity of aquatic systems as a whole, including the HZ, rather than independently focusing on SW and GW.