Under certain hydrological conditions it is possible for spring flow in karst systems to be reversed. When this occurs, the resulting invasion by surface water, i.e. the backflooding, represents a serious threat to groundwater quality because the surface water could well be contaminated. Here we examine the possible impact of future climate change on the occurrences of backflooding in a specific karst system, having first established the occurrence of such events in the selected study area over the past 40 years. It would appear that backflooding has been more frequent since the 1980s, and that it is apparently linked to river flow variability on the pluri-annual scale. The avenue that we adopt here for studying recent and future variations of these events is based on a downscaling algorithm relating large-scale atmospheric circulation to local precipitation spatial patterns. The large-scale atmospheric circulation is viewed as a set of quasi-stationary and recurrent states, called weather types, and its variability as the transition between them. Based on a set of climate model projections, simulated changes in weather-type occurrence for the end of the century suggests that backflooding events can be expected to decrease in 2075–2099. If such is the case, then the potential risk for groundwater quality in the area will be greatly reduced compared to the current situation. Finally, our results also show the potential interest of the weather-type based downscaling approach for examining the impact of climate change on hydrological systems.