Maerl beds are ecologically important marine biogenic habitats founded on a few species of free-living coralline algae that aggregate and form highly complex rhodoliths. The high biodiversity found in these habitats have been mainly justified by the structural complexity that they provide. However, few attempts to quantify this complexity have been made. Maerl species distribution, density, rhodolith growth forms, and shapes vary with environmental conditions. Hydrodynamics and depth have been shown to drive morphology. Using species-specific metrics such as sphericity and branching density, as well as diameter and fractal dimension at the rhodolith level, and maerl density at the habitat level, we quantified the habitat complexity within ten maerl beds at a regional scale (along ∼400 km of the coastline of Brittany in Western France). Using both long-term monitoring data and environmental models, we investigated how maerl habitat complexity varies among beds and which environmental conditions drive those differences. The effects of currents, exposure to wind-generated waves, temperature and sediment granulometry were evaluated. We confirmed variations in complexity in maerl beds at the habitat and rhodolith levels at local and regional scales, which might have ecological and conservational implications for their associated biodiversity. The analysed environmental conditions drive around a third of the variance in habitat complexity. Sediment granulometry is the main driver of maerl habitat complexity in Brittany, while the isolated effects of depth and hydrodynamics accounted for less than 5% of the variability each. Our results have important implications for paleoecology, and we suggest that maerl facies should be interpreted carefully. Our study provides a first attempt at explicitly quantifying maerl habitat complexity, and further contributes to the understanding of this fundamental ecological question.