Atmospheric nutrient deposition has contributed to widespread changes in sensitive seminatural ecosystems throughout Europe. For an understanding of underlying processes it is important to quantify input–output flows in relation to ongoing atmospheric inputs and current management strategies. In this study we quantified losses of N, P, Ca, Mg, and K via leaching in heathland ecosystems (Lüneburger Heide, NW Germany) as a function of current deposition rates and different management measures (mowing, prescribed burning, choppering, sod-cutting) which aim to prevent shrub and tree encroachment. Leaching was only moderately related to atmospheric input rates, indicating that leaching was mostly affected by internal turnover processes. Leaching significantly increased for most of the nutrients after the application of management measures, particularly in the choppered and sod-cut plots. However, atmospheric nutrient inputs exceeded leaching outputs for most of the nutrients, even in the plots subjected to management. Despite high deposition rates (20–25 kg N ha−1 year−1), retention of atmospheric N input ranged between 74% and 92% in the control plots. In the treated plots, N retention decreased to 59–80%. However, in the study area mean N leaching in the controls has almost doubled since 1980 and currently amounts to 3.7 kg ha−1 year−1, indicating an early stage of N saturation. Our study provides evidence that leaching did not compensate for atmospheric nutrient deposition, particularly as regards N. Management, thus, will be an indispensable tool for the maintenance of the low-nutrient status as a prerequisite for the long-term preservation of heathland ecosystems.