The transport of nutrients into water bodies is one of the main causes of water eutrophication. It is therefore important to estimate the loads of nutrients. Discharge and nutrient concentrations are the fundamental elements to estimate the loads of nutrients, the latter can be affected by sampling strategies. As conducting sampling campaign and laboratory analysis are both expensive, it is necessary to find the best effective sampling strategy. The aim of this paper is to show how autocorrelation and standard statistical methods can be used to test the effects of different sampling strategies on the nutrient load estimation and to find the optimal sampling strategy. The data set in this study is from the 50 km² Kielstau catchment, a UNESCO demo site for ecohydrology in Northern Germany and consists of 14 years daily values of climate, hydrology, and water quality from 2006 to 2019. We calculated the autocorrelation (AC) of discharge (Q), precipitation, Nitrate-Nitrogen (NO3-N) and total Phosphorus (Ptot). Then we tested the effects of sampling intervals from 7 to 56 days (1–8 weeks) on the nutrient loads. Our results showed a high AC of Q and NO3-N for a long period, but the AC of Ptot and precipitation decreased very fast. An increase of the sampling interval (less frequent) increased the error of estimating the concentrations and loads. Consequently, we recommend that (1) the optimal sampling strategy for nutrient load estimation in an agriculture-dominant catchment should be continuously monitoring discharge combined with periodic grabbed samples; (2) the sampling frequency for NO3-N is suggested to be monthly (every 28 days) and for Ptot weekly (every 7 days). The information will help those tasked with catchment monitoring to design appropriate sampling strategy to ensure adequate data for nutrients load estimation in lowland rivers.