We demonstrate serial electron transport through a donor-based triple quantum dot in silicon fabricated with nanoscale precision by scanning tunnelling microscopy lithography. From an equivalent circuit model, we calculate the electrochemical potentials of the dots allowing us to identify ground and excited states in finite bias transport. Significantly, we show that using a scanning tunnelling microscope, we can directly demonstrate that a ∼1 nm difference in interdot distance dramatically affects transport pathways between the three dots.