Daily time series were used to verify the temporal variability and to characterize the nitrogen (N) and phosphorus (P) pollution in a 462 km² catchment of the Stör river, a typical rural lowland catchment in Germany. Also, this study aimed to identify the best sampling frequency of pollution by N and P. Total phosphorus (TP), soluble orthophosphate-phosphorus (PO4-P), particulate-phosphorus (PP), total nitrogen (TN), nitrate-nitrogen (NO3-N) ammonium-nitrogen (NH4-N) and total suspended sediment (TSS) were analysed. Daily monitoring from August 8, 2009 until August 10, 2011 was conducted with an automatic water sampler at the outlet of the catchment. The results show a seasonal variability of water quality parameters with more N and P concentration in winter. PP represents the major part of P and it is highly dependent on TSS. NO3-N constitutes the major part of N. Autocorrelation analysis was successfully applied to characterize the N and P pollution in the Upper River Stör. The water sampling for N and P monitoring must be different, N can be sampled biweekly or monthly, while P must be sampled with more frequency, weekly or biweekly.