Aggregation-based crystal growth often gives rise to crystals with complex morphologies which cannot be generated via classical growth processes. Despite this, understanding of the mechanism is rather poor, particularly when organic additives or amorphous precursor phases are present. In this work, advantage is taken of the observation that aggregation-based growth of calcium carbonate, and indeed many other minerals, is most often observed using diffusion-based synthetic methods. By fully characterizing the widely used ammonia diffusion method (ADM)–which is currently used as a “black box”–the solution and supersaturation conditions which accompany CaCO3 precipitation using this method are identified and insight is gained into the nucleation and growth processes which generate calcite mesocrystals. This reveals that the distinguishing feature of the ADM is that the initial nucleation burst consumes only a small quantity of the available ions, and the supersaturation then remains relatively constant, and well above the solubility of amorphous calcium carbonate (ACC), until the reaction is almost complete. New material is thus generated over the entire course of the precipitation, a feature which appears to be fundamental to the formation of complex, aggregation-based morphologies. Finally, the importance of this understanding is demonstrated using the identified carbonate and supersaturation profiles to perfectly replicate CaCO3 mesocrystals through slow addition of reagents to a bulk solution. This approach overcomes many of the inherent problems of the ADM by offering excellent reproducibility, enabling the synthesis of such CaCO3 structures in large-scale and continuous-flow systems, and ultimately facilitating in situ studies of assembly-based crystallization mechanisms.