AbstractArtificial substrates buried in stream sediments at the karst/floodplain interface were used to examine the spatial and temporal variations ofNipharguspopulations. The study was carried out at two stations in two different areas of the French Jura. One was mainly supplied by karst water (Verna station), the other by both karst and surface waters (Pissoir station). The occupation of interstitial habitat was found to depend on several interacting factors:1The waterflow and its changes at the outlet. The correlation between abundance of individuals and discharge was strongest with the discharges two to four days before sampling. The structure and restoration of populations after a spate related to geological characteristics. In particular, restoration was slower and more difficult in the sediments located at the base‐level of a massif (Verna) than at an overflow level (Pissoir).2The location of the sediments. At the Pissoir station, the number of individuals was higher at the main outflow, but also for both stations, on the banks opposite the outlet. Animals drifting from the karst system found refuge in the sediment of the opposite bank. Almost noNipharguswere found upstream from the outlets. At the Verna station,Nipharguswere only found inside the cave.3The variability of the number of animals at different depths in the sediment was more difficult to explain. At the station mainly supplied by karst water, which presented a relatively constant flow during the study, the distribution seemed to be random. At the other station, where discharge varied considerably, the vertical distribution globally presented a gradient in abundance with more individuals in the upper sediment level. This gradient varied according to the samples. Discharge changes partly explained these result