Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed twelve grow outs of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is specified developmentally and influenced by water availability and planting density. The non-destructive nature of plant height measurement has enabled us to monitor vertical growth throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by experimental environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the identity of the major genetic loci that influence plant height are not dependent upon growth environment. The contribution of individual genetic loci that influence height change dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in Setaria. In this population, alleles inherited from the weedy S. viridis parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated S. italica parent increase plant height later in development.