To quantify nutrients discharged from agricultural fields under different manure application practices, six field stations were installed to automatically sample water and remotely monitor flow and temperature in agricultural tile drains and ditches. Each station included a datalogger, RF radio, automated sampler, and flow sensor, with some remote stations powered by solar panels. A novel sampling methodology, tested at two of the stations, used real-time volumetric flow data as input to a hydrograph model encoded in the datalogger to generate hydrograph-specific sampling schemes for sampling at different flow-proportional frequencies. This unique sampling methodology produced high-resolution data independent of the hydrograph size, providing additional insight into how environmental processes influence the quality and quantity of flow from an agroecosystem on an event-by-event basis. An initial assessment of the results suggests that the relative importance of environmental controls on the transport of nitrogen and phosphorus exhibits high temporal variability.