Abstract: Photozoan and heterozoan carbonate systems differ in their biotic assemblages and depositional facies distribution. These, in turn, control their response to relative sea-level change, which affects stratigraphic architecture. Understanding the controls over the occurrence of different carbonate types is important when interpreting the fossil record. The differentiation of carbonate systems today into photozoan and heterozoan assemblages is directly dependent on the environmental requirements of the biocalcifiers active in the modern world. Because biocalcification mechanisms and environmental requirements have changed through time, it becomes increasingly difficult to apply this differentiation to older carbonate systems. This paper reviews general controls over the distribution of biotic assemblages in the modern world, investigating the major limiting factors affecting carbonate assemblages. Selected examples from icehouse and greenhouse time intervals are also discussed to highlight the effects of major limiting factors in the geological past. Icehouse times are characterized by stronger temperature and nutrient gradients, with environments spanning a larger spread of possible conditions. Times of climatic changeover are recorded by broad community shifts from the photozoan to heterozoan–photozoan transition. Greenhouse times, conversely, are characterized by gentler temperature gradients and biota suggesting that mesotrophic conditions were more widespread. This translates to a higher chance to find an expanded occurrence of heterozoan–photozoan transitional settings. Carbonate systems, with their unique biological and geochemical characterization, have a still largely unexplored potential to provide a record of Earth history events that have no modern analogues. However, it is critical to be fully aware of the factors and processes operating at different timescales that have an effect on biogenic assemblages and carbonate systems. The use of the terms photozoan and heterozoan must be used very critically going back in time. Rather than simply applying one model, the intrinsic complexities of carbonate systems require a detailed understanding of how and where sediment is produced, and eventually transported and deposited, before reliable paleoenvironmental scenarios can be constructed.