Karst aquifers in subtropical regions are characterized by high variability of water availability and quality due to changes associated with rainy and dry seasons. An additional challenge for water management is the combination of surface-water and karst groundwater systems since high spatiotemporal dynamics cause high variability of water quality. In these cases, adapted protection strategies are required. In this study, a protection approach for the catchment of a river-water diversion point in a rural area in northern Vietnam is developed. The variability of water quality was evaluated by rainy and dry season synoptic surveys of suspended particles and microbial contamination at 49 sites and time series at three sets of paired sites under constant hydraulic conditions. The anthropogenic land-use activities in the catchment were mapped to identify potential contamination sources and to highlight the challenging combination of surface-water and karst groundwater management. The analyzed data indicate differences in water quality between the dry and rainy seasons and a higher influence on water quality from land use than from hydrologic conditions. ... mehrFurthermore, the results suggest a high risk of contamination resulting from residential areas, agriculture, and livestock farming, and reveal the necessity of implementation of appropriate measures such as restricted farming and the hook-up of buildings to municipal sewage disposal. Finally, the data show that water quality can be improved by adjusting water withdrawals by the time of day. The applied methods can be transferred to other surface-water and karst groundwater systems in similar subtropical environments.