The hyporheic zone (HZ) is vital for nutrient cycling and overall stream ecosystem health across groundwater-surface water interfaces, with biogeochemical and physical variations influencing exchange processes. To gain a depth-oriented insight into the various hyporheic functioning, isotopic (18O and 2H) and chemical analyses, along with physical parameters, were performed in two streams named Ahna and Losse in North Hesse, Germany. Multi-level interstitial probes were installed to extract subsurface pore water samples up to 0.45 m depth. We identified three distinct HZ in Ahna upstream, downstream and Losse. The Ahna upstream HZ was a less permeable barrier with low water fluxes but reactive, while the downstream HZ was less reactive with higher permeability and vertical fluxes. The Losse HZ, remained non-reactive but well-mixed with good hydraulic circulation due to fast downward flows. Isotopic composition revealed distinctive features, indicating increased evaporation and intricate mixing with other water sources and intensified subsurface flow in Ahna downstream compared to upstream. Hydro-chemical dynamics in Ahna exposed increased ion concentrations downstream, driven by anthropogenic factors along the course. Upstream denitrification was dominant under low oxygen conditions due to the slow infiltration and low mixing rates. The primary water source for both streams and HZs was groundwater, with the potential for rainwater to serve as a secondary source. This study shows the spatial heterogeneity of HZ processes and highlights that the specific HZ conditions need to be examined locally.