This investigation deals with the application of a multi-technique approach combining data from turbidity, major ions, and trace elements to characterize the implications of allogenic recharge in a binary karst system and assess the relative hydrochemical contribution to karst springs captured for drinking use. Hydrodynamic and hydrochemical responses of the outlets to storm events were continuously monitored during four selected flooding events, and water samples were collected at the main sinking stream in the recharge area and discharge points (Cornicabra and Algarrobal springs) for chemical analysis. The obtained hydrogeochemical dataset was analyzed through mean of time-series and statistical analysis and allowed to describe the fate and origin of trace elements. Despite that most of analyzed components present a natural origin, the existence of a Wastewater Treatment Plant in the recharge area was determined to be the main source of P (phosphorus) concentrations measured in the karst springs. Sediment (particulate) transport constitutes the most important factor in the mobilization of Al, Mn, Ni, and Ba in both surface and groundwater, whilst Li, Sr, and P are mainly controlled by solute migration. The hydrochemical signature of allogenic water component was constrained by identifying characteristic correlations between Ba and Ca/Sr ratio in water samples. The combination of specific hydrogeological processes as ion solution and sorption processes onto solids between solutes and particles as well as water mixing processes (allogenic vs diffuse) result more evident in Algarrobal spring, which receives a higher contribution of allogenic component due to a greater feeding catchment.