At basin scale the physical phenomenon of diffusion involves the intricate spreading and dispersion of substances within complex systems as networks of interconnected channels, streams, and land surfaces. Understanding this process is crucial for many purposes as management and conservation of water resources. We extend the model application of our previous work (Part I, Rizzello et al. in Stoch Environ Res Risk Assess 37:3807–3817, 2023) from channel to basin scale. We use conservation of mass and momentum to formulate and apply the Master Equation system at basin scale. The results on simulated events highlight the transition of the model from channel scale to basin scale.