Reducing excessive reactive nitrogen (N) in agricultural waterways is a major challenge for freshwater managers and landowners. Effective solutions require the use of multiple and combined N attenuation tools, targeted along small ditches and streams. We present a visual framework to guide novel applications of ‘tool stacking’ that include edge-of-field and waterway-based options targeting N delivery pathways, timing, and impacts in the receiving environment (i.e., changes in concentration or load). Implementing tools at multiple locations and scales using a ‘toolbox’ approach will better leverage key hydrological and biogeochemical processes for N attenuation (e.g., water retention, infiltration and filtering, contact with organic soils and microbes, and denitrification), in addition to enhancing ecological benefits to waterways. Our framework applies primarily to temperate or warmer climates, since cold temperatures and freeze–thaw-related processes limit biologically mediated N attenuation in cold climates. Moreover, we encourage scientists and managers to codevelop N attenuation toolboxes with farmers, since implementation will require tailored fits to local hydrological, social, and productive landscapes. Generating further knowledge around N attenuation tool stacking in different climates and landscape contexts will advance management actions to attenuate agricultural catchment N. Understanding how different tools can be best combined to target key contaminant transport pathways and create activated zones of attenuation along and within small agricultural waterways will be essential.