The objectives of this paper were to introduce frameworks for predicting the determinants and consequences of the great heterogeneity in benthic algal assemblages. A hierarchical framework of environmental factors affecting benthic algal spatial heterogeneity is presented with the ultimate determinants (climate, geology, land use, and biogeography) that are important constraints on benthic algal assemblage structure at large spatial scales. These ultimate determinants constrain expression of intermediate and proximate determinants of benthic algal function and structure. A similar framework for temporal heterogeneity distinguishes how assemblages respond to short-term and long-term environmental changes, referred to as disturbances and stresses, respectively. Assemblages recover from punctuated (short-term) environmental change (disturbance) by immigration and reproduction of both persistent and recolonizing species. Assemblages adapt to permanent (long-term) environmental change (stress) by changing species membership, i.e., loss of some species that cannot survive in the new conditions and invasion of new species that are adapted to the new conditions. Stresses operating on large temporal scales probably constrain effects of disturbance, which operate on small temporal scales. The consequences of interactions among patches are related to benthic algal assemblages and are referred to as the emergent properties of heterogeneity. Enhanced biomass, diversity, and stability of benthic algae are hypothesized to be emergent properties of habitat heterogeneity. A mathematical model is presented that indicates that algal accrual in a reach is enhanced by interactions between algae in riffles and pools. Conceptual models are introduced that hypothesize that dispersal in spatially and temporally heterogeneous habitats enhances diversity and stability of benthic algal assemblages.