Abstract Network particle tracking (NPT), building on the foundation of network environ analysis (NEA), is a new development in the definition of coherence relations within and between connected systems. This paper evaluates three ecosystem models in a comparison of throughflow- and storage-based NEA and NPT. Compartments in models with high indirect effects and Finn cycling showed low correlation of NEA storage and throughflow with particle repeat visits and numbers of particles in compartments at steady state. Conversely, the correlation between NEA and NPT results was high with two models having lower indirect effects and Finn cycling. Analysis of ecological orientors associated with NEA showed NPT to fully support conventional NEA results when the common conditions of donor control and steady state are satisfied. Particle trajectories are recorded in the new concept of a particle “passport”. Ability to track and record particle in-system histories enables views of multiple scales and opens the possibility of making pathway-dependent modeling decisions. NPT may also enable modeling of time, allowing integration of Newtonian, organismal and stochastic modeling perspectives in a single comprehensive analysis.