Because of their significant public health impact, waterborne Cryptosporidium and Giardia have been monitored in surface water in order to assess microbial quality of water bodies used for drinking water production and/or for recreational purposes. In this context, sampling strategy is of key importance and should be representative enough to appropriately assess the related microbial risk. This, however, requires sound knowledge on the behaviour of both pathogens in water. In the present study, the spatial and temporal distribution of Cryptosporidium and Giardia was explored in the rural Upper-Sûre watershed used for drinking water production in Luxembourg. By subdividing it into three compartments including (i) sub-catchments, (ii) the Sûre River fed by the sub-catchments and (iii) the Upper-Sûre reservoir fed by the Sûre River, parasite distribution was assessed using sampling designs adapted to the hydro-dynamic characteristics of the respective compartments. Results highlighted the high spatial and temporal variability in parasite distribution at watershed scale, as well as the prevalence of Giardia over Cryptosporidium. Besides land use features and catchment characteristics, hydro-climatology appeared to be a major driver of parasite behaviour in the watershed. It introduced a seasonal trend in their occurrence, highest densities being detected during the wet season. Peaks of contamination triggered out by rainfall-induced runoff were further observed in the three compartments. In the Sûre River, Cryptosporidium and Giardia fluxes peaked at 10 9 and 10 10 (oo)cysts.d −1 , respectively, and were discharged into the drinking water reservoir, where they underwent a 2 to 3 log 10 removal rate. Despite this, parasite fluxes entering the drinking water treatment plant were still high (10 6 to 10 7 (oo)cysts.d −1 ) and stressed on the need for improved watershed management upstream the water treatment barrier. The catchment-wide analysis described here constitutes a valuable tool for assessment of catchment microbial dynamics, especially within the framework of Water Safety Plans.