Groundwater pollution with nitrate is a big challenge for drinking water abstraction in regions with intensive agricultural land-use, specifically with high livestock densities on sandy soils in humid climates. Karst aquifers with high water flow velocities are extremely vulnerable to this problem. To cope with this situation, a field trial with an installation of ceramic suction cups under a randomised block design with a typical north-German cropping sequence of silage maize–winter wheat–winter barley was established in a karst water protection zone. Over three years, reduced nitrogen (N) application rates and N type (mineral or combined organic + mineral fertilisation) were tested for their effects on crop yields and leachate water quality below the root zone. Results showed no significant reductions in crop yields with 10/20% reduced N rates for cereals/maize and only slight reductions in cereal protein content. Nitrate concentration from adapted N rates was significantly lower in treatments with an application of organic fertilisers (−7.74 mg NO₃-N l⁻¹) with greatest potential after cultivation of maize; in only mineral fertilised plots the effect was smaller (−3.80 mg NO₃-N l⁻¹). Cumulative leaching losses were positively correlated with post-harvest soil mineral nitrogen content but even in unfertilised control plots losses >50 kg N ha⁻¹ were observed in some crop-years. Reduced N rates led to decreased leaching losses of 14% (6.3 kg N ha⁻¹ a⁻¹) with mineral and 29% (20.1 kg N ha⁻¹ a⁻¹) with organic + mineral fertilisation on average overall cops and years. The presented study revealed the general potential of adapted fertilisation strategies with moderately reduced N applications (−10/−20%) to increase leachate water quality without affecting significantly crop yields. However, regionally typical after-effects from yearlong high N surpluses in livestock intensive farming systems are a limiting factor.