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Most studies on the effects of tillage operations documented the effects of tillage on losses through surface runoff. On flat areas, the subsurface runoff is the dominating pathway for water, soil and nutrients. This study presents results from a five-year plot study on a flat area measuring surface and subsurface runoff losses. The treatments compared were (A) autumn ploughing with oats, (B) autumn ploughing with winter wheat and (C) spring ploughing with spring barley (n = 3). The results showed that subsurface runoff was the main source for soil (67%), total phosphorus (76%), dissolved reactive phosphorus (75%) and total nitrogen (89%) losses. Through the subsurface pathway, the lowest soil losses occurred from the spring ploughed plots. Losses of total phosphorus through subsurface runoff were also lower from spring ploughing compared to autumn ploughing. Total nitrogen losses were higher from autumn ploughing compared to other treatments. Losses of total nitrogen were more influenced by autumn ploughing than by a nitrogen surplus in production. Single extreme weather events, like the summer drought in 2018 and high precipitation in October 2014 were crucial to the annual soil and nutrient losses. Considering extreme weather events in agricultural management is a necessary prerequisite for successful mitigation of soil and nutrient losses in the future.