Karst aquifers have been globally exploited as a reliable source of drinking water but their intrinsic characteristics (concentrated recharge, high groundwater flow velocities, etc.) and the increase of anthropogenic pressures makes them highly vulnerable to pollution. Continuous monitoring of karst springs constitutes an effective approach for identifying episodic groundwater contamination and assuring safety conditions in drinking water supply systems. This study aims to improve groundwater protection insights through an integrated methodological approach based on real-time measurements of continuous water parameters coupled to bacterial analysis for the characterization of contamination events in a carbonate karst aquifer of a mountainous and rural area in S Spain. For this purpose, environmental, hydrodynamic and physico-chemical data in addition to bacterial activity (Escherichia coli) analysis were gathered from the analysis of eight flooding events at the two main outlets. In these karst springs, partially captured for drinking water supply, the recurrent turbid groundwater episodes suppose an important limitation for groundwater exploitation during several days, but also a concerning human health risk. The results revealed the different flow and sediment dynamics and mixing processes which determine the impact of faecal contamination derived from human activities on the karst groundwater drained by each spring. The described processes control the variable influence of allogenic recharge, which provokes notable differences regarding response times and maximum values of turbidity and associated bacterial activity in the investigated outlets. The outcomes of this work highlight the usefulness of the applied methodological framework to set the bases for an efficient implementation of early-warning strategies to prevent public health issues worldwide. Display omitted •An approach for early detection of karst groundwater faecal contamination is presented.•Continuous monitoring of climate and water parameters was coupled to bacterial analysis.•Sediment source contribution to the karst springs was qualitatively assessed.•Human activities were responsible for the faecal bacteria detected at drinking water sources.•Site specific karst groundwater protection strategies are crucial to prevent public health issues.