Analysis of 500 km of multichannel seismic reflection data in the Southern Lagoon of Belize reveals that its Tertiary structural evolution has been punctuated by two major transtensional episodes. First, left-lateral strike-slip motion parallel to the coast, together with a major component of extension, took place during the Paleocene, producing a series of southwest-northeast-trending en echelon normal faults, which created a topographic relief of ridges and troughs. Both the types of structures and their timing of formation are consistent with models that propose that Cuba swept past the eastern coast of Belize and the adjacent Yucatan peninsula, moving along a left-lateral transform boundary, until it collided with the Bahamas platform.

The second tectonic event occurred during the Pliocene and/or later, revealing very recent activity along the North American-Caribbean left-lateral transform boundary. High-angle normal faults with a southwest-northeast orientation dominate the style.

A comparison between the deep structure and the present bathymetry of the lagoon reveals that portions of the barrier platform and elongate to rhombohedral platform atolls, such as Laughing Bird Cay, are located over ancient structural highs, whereas bathymetric lows, such as the Victoria Channel, are long-lived troughs. This suggests that Quaternary reef foundations are deeper than previously thought, and that structure exercised a major control on sedimentation throughout the Tertiary evolution of the Southern Lagoon.