The design of productive and efficient intercropping agroforestry systems, which minimise environmental pollution, depends on achieving complementarity between component species' resource capture niches. This concept was tested by assessing spatiotemporal patterns of vertical and Lateral water and N capture and use by trees and intercrops in agroforestry systems in Indonesia. Using trees to provide a biological root safety-net in intercropping systems, will only be successful if trees do not adversely affect crop growth. Sensitivity analyses using the dynamic agroforestry model WaNuLCAS suggested that N interception efficiency increases with tree root Length density and depth of soil in the safety-net Layer. However, N interception efficiency is Limited by tree N demand, and it decreases as the proportion of tree N derived from atmospheric fixation increases. Hence non-N-2 fixing trees may provide a more effective safety-net for N. Thus the current perception of the ideotype, fast growing, N-2 fixing, agroforestry tree has to be revised towards a slower growing, but drought resistant species, that is deep rooting with few active topsoil roots and which produces slowly decomposing pruning residues. Scaling up these concepts offers opportunities for enhancing the filter efficiency of farms by appropriate selection and positioning of agroforestry options within the landscape.