Exchange of water in the parafluvial zone, located along the boundaries of meandering streams, arises in response to seasonal variation and spatial distribution. Remarkably, few studies have applied multi-tracer methods for qualitative scrutiny of losing (recharge) or gaining (discharge) reaches along the parafluvial zone. Hence, the main objective of this study is to qualitatively characterize the spatio-temporal alteration in parafluvial exchange within the hyporheic zone (PEHZ) by simultaneous application of multi-tracer methods. For this approach, first, Hierarchical Cluster Analysis (HCA) in conjunction with groundwater hydrochemistry analysis was used to evaluate the representativeness of parafluvial assessment network. Then, water stable isotope compositions (δ¹⁸O and δ²H), radioisotope (²²²Rn), and environmental tracers (Temperature and EC) were measured at multiple depths (20 cm to 100 cm depths below streambed) during the wet and dry season to qualitatively elucidate the PEHZ in the Ghezel-Ozan River, a third order river located in the northwest of Iran. By groundwater hydrochemistry assessment identified, NaHCO₃ and CaHCO₃ as the dominant water type in dry and wet season, respectively. Moreover, the HCA approach designed two different clusters for each season for accurate interpretation of PEHZ. Results obtained from stable isotope and environmental tracer analysis of bore water, surface water, and parafluvial water distinguished stream-aquifer connectivity with highly seasonal and spatial variations. In the dry season, for example, δ¹⁸O, δ²H, and EC varied from −3.59 to −1.88 (‰ VSMOW), −31.08 to −24.06 (‰ VSMOW), and 234 to 740.65  μS/cm respectively. Also, the results acquired from the integration of δ¹⁸O and EC revealed complex spatio-temporal stream-aquifer connectivity (PEHZ). In low flow conditions, groundwater outflow mainly occurred at 100 cm depth while the dominance of groundwater outflow at 20 cm depth prevailed during high flow conditions. The continuous and point scale measurements of temperature and ²²²Rn were highly in accordance with the results of δ¹⁸O and EC. Furthermore, diel temperature fluctuation, as well as radon activity variations at multi-level scale, expressed the PEHZ (especially at depth greater than 60 cm) are affected by large-scale regional flow-field which is embedded within. The synthesized approaches used in this study provide a useful insight into the spatiotemporal changes of stream-aquifer connectivity which make the more efficient monitoring and interpretation of hydrological processes possible. They can be, furthermore, utilized to pinpoint the losing/gaining reaches accurately to tackle environmental problems such as monitoring the transport of anthropogenic contaminants in a system.