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Mobile particles play crucial roles for contaminant transport in karst aquifers, but few studies have investigated the relationships between sediment dynamics and contaminants. This is partly due to the difficulty in monitoring suspended particles: Turbidity is easy to measure but does not deliver detailed information on the size and type of particles; mineralogical laboratory analyses are laborious and not suitable for continuous monitoring. A portable particle counter was used for the study presented here. The instrument delivers time-series of particle-size distribution (PSD), i.e. the number and diameter of suspended particles, grouped into different size-classes ranging from 0.9 to 139 μm. The test site is a karst system near the city of Yverdon-les-Bains, Switzerland. A swallow hole draining agricultural land is connected to two karst springs, 4.8 and 6.3 km away, which are occasionally contaminated by faecal bacteria at highly variable levels. Turbidity alone turned out not to be a reliable indicator for microbial contamination. To obtain more insight into bacteria and particle transport towards the springs, a comprehensive research program was carried out, including tracer tests and monitoring of PSD, turbidity, total organic carbon (TOC), faecal bacteria(E.coli) and various hydrologic and physicochemical parameters. Results show that there are two types of turbidity: A primary turbidity signal occurs shortly after rainfall during the rising limb of the hydrograph; a secondary signal typically occurs during spring flow recession. The first signal is explained by remobilization of conduit sediments due to a hydraulic pressure pulse (autochthonous or pulse-through turbidity). The second peak indicates the arrival of water from the swallow hole, often together with TOC and faecal bacteria (allochthonous or flow-through turbidity). PSD analyses revealed that autochthonous turbidity is composed of a broad mixture of fine and large particles, while allochthonous turbidity predominantly consists of very fine particles. This is explained by sedimentation of larger particles between the swallow hole and the springs. During allochthonous turbidity periods, very good correlation between the finest particles (0.9–1.5 μm) and E. coli was found (R2 = 0.93). The relative increase of fine particles can consequently be used as an “early-warning parameter” for microbial contamination of karst spring water. Further applicability and limitations of this approach are also discussed.