The movement of matter is observable (although it can be tricky) and extensively studied/measured as gas exchange rates (e.g., between soil and atmosphere), hydraulic conductivity of soils, water flow in rivers, leaching of nutrient elements, lessivage (transport of fine solid particles), soil erosion, etc. The energy flow cannot be seen directly. It is an abstraction inferred (calculated) from diverse experimental data (food consumption, population size, growth rates, elimination, biochemical basics) and based on thermodynamics, conservation law and some more specific assumptions.