Reef communities changed dramatically during the Early Jurassic as they recovered from the End-Triassic Mass Extinction. The Atlas Rift Zone in Morocco provided expansive shallow water substrate, which allowed a variety of reef communities to develop, such as lithiotid bivalves that established themselves as new and prolific reef builders alongside corals, microbialites, and sponges in the Sinemurian and Pliensbachian stages. To better understand the dynamics between these reef builders and their environments, a detailed facies analysis of upper Pliensbachian reefs and a quantitative analysis of their composition was undertaken. We describe two distinct environmentally controlled reef types in the Central High Atlas Mountains. Lithiotid bivalves dominated reef construction in lagoonal environments and, together with phaceloid corals, commonly built bioherms and biostromes that ranged from 1 to 2 m tall and up to several hundred meters wide. Meanwhile, on the platform edge, microbialites, corals, and sponges constructed patch reefs up to 7 m tall and 20 m wide. These two reef types share common facies, as many of the same reef inhabitants, and some framework builders, grew in both environments. Despite the facies overlap, the communities in these two environmental settings are distinct, which is likely a result of environmental controls on the dominant reef framework builders. Moderately turbid waters and soft substrate in lagoons were ideal conditions for lithiotids but excluded many corals, sponges, and microbialites. Conversely, the clear, oligotrophic waters at the platform edge allowed photosynthetic and photosymbiotic organisms to thrive (e.g., coral and microbial reefs), while firmer substrate and higher wave energy may have prevented lithiotids from establishing dense populations.