The present study examined the dynamics of nitrate pollution in springs and headwater streams in agriculturally used watersheds. The objectives of the study were to record the pollution dynamics throughout the year as a function of different weather patterns and determine the correlation of these dynamics with the degree of agricultural use of the relevant catchments. Moreover, continuous measuring methods should be compared with regular manual sampling procedures.Seven springs with agricultural catchments and their headstreams were studied over 2 years, as well as a reference water body with a forested catchment. At two of the springs, continuous measurements were additionally performed using ion-selective electrodes. Two agrometeorological stations were installed to record the relevant weather parameters.Every water body with agriculturally used surroundings exhibited increased nitrate values. A significant correlation was found between the NO3− concentration and the proportion of arable land in the catchment. The nitrate concentration dynamics exhibited extreme weather-related and seasonal fluctuations. While nitrate maxima in autumn and winter correlated widely with the precipitation curve, heavy rainfall in spring and summer led only to short concentration peaks, followed by lower values, presumably caused by dilution effects. Between the spring and downstream measuring points, the nitrate loads increased by the same extent as the arable land area primarily responsible for their emission. No clear nitrate retention was observed between the springs and headstream measuring points. Grab sampling appeared to be sufficiently accurate to record nitrate concentrations when performed at monthly intervals over a two-year measurement period. However, continuous discharge measurements in parallel seemed necessary to determine the loads. The year of 2015 was characterized by a much drier summer and wetter winter, with universally higher nitrate pollution. If these conditions become more established as climate change progresses, increased nitrate pollution must be expected in future.