This study examined the influence of rainfall-runoff events on water quality of the Upper Catchment of the Jordan River (UCJR) with a special emphasize on P fate and transport. We sampled 60 locations across the catchment to test the hypothesis that under Mediterranean climate conditions, most of the nutrient losses from the fields to waterways will occur in few major events while the actual contributing areas will be limited to critical source areas (CSA). Water analyses included nutrients (SRP, TP, TSS, NO3, & NH4), fecal indicators (Fecal Coliforms, E-Coli and Enterococcus) and EC & pH. Spatial analysis was conducted to identify CSA. In general, the results demonstrated the influence of runoff events on the water quality in the UCJR and the high heterogeneity of these events in space and time. The study showed that the levels of SRP, TP, TSS as well as indicators of fecal contamination were primarily transported with surface runoff and increased significantly in the stream during these events. Phosphorous concentrations in some sub-catchments reached extremely high concentrations (19 mg/l) during runoff compared with an average of 1.9 mg/l for the entire watershed. The medium to high correlation between the fecal indicators, total P and TSS suggest that during runoff events, P and bacteria attached to soil particles were mobilized to the stream from CSA. Water sampling along the streams flow paths together with the spatial analysis, identified CSA where an elevated nutrient concentration has been identified. Autocorrelation test identified CSA where an external pollution source influences the water nutrients content. The study provides watershed management science-based remediation options to reduce the potential of water pollution during major rainfall-runoff events. © Springer International Publishing Switzerland 2016. All rights are reserved.