Soil aggregation and its effects on soil C storage have been addressed in thousands of research articles over the last 40 years. Research has been mostly focused on the resistance of aggregates to mechanical disruption and the role of organic matter in aggregate stabilization. On the other hand, relatively little attention has been paid to identifying the microbial, plant root and macro-invertebrate actors and physical processes that continuously create and destroy aggregates. The sum and dynamics of these processes determines the ability of soils to store and conserve C. Understanding the interactions between aggregation dynamics and C transformations in soils therefore requires a precise identification of the agents that produce aggregates and knowledge of the rates of formation and persistence in the pools thus identified. We propose to separate macro-aggregated components of different, physicogenic and biogenic origins from non-macro-aggregated soil on a morphological basis, using a simple visual technique. The specific biological or physico-chemical agent which produced each individual macro-aggregate can then be determined using Near Infrared Spectroscopy (NIRS). A general description of the distribution and quality of organic matter among the different groups of macro-aggregates can be made. Simple soil re-aggregation or dis-aggregation tests conducted in field conditions further measure the production of different macro-aggregates with time and their mean residence times in the studied soil. Respirometry measurements on each recognized category of macro-aggregates evaluate the respective C losses through respiration. The methods described here will allow the dominant pathways of C flow at a given site to be characterized and possible management options to increase C storage identified. We finally discuss the different assumptions made to build this simple model and offer ways to test the methodology under field conditions.