Natural convection arising over vertical and horizontal heated flat surfaces is one of the most ubiquitous flows at a range of spatiotemporal scales. Despite significant developments over more than a century contributing to our fundamental understanding of heat transfer in natural convection boundary layers, certain “hidden” characteristics of these flows have received far less attention. Here, we review scattered progress on less visited fundamental topics that have strong implications to heat and mass transfer control. These topics include the instability characteristics, laminar-to-turbulent transition, and spatial flow structures of vertical natural convection boundary layers and large-scale plumes, dome, and circulating flows over discretely and entirely heated horizontal surfaces. Based on the summarized advancements in fundamental research, we elaborate on the selection of perturbations and provide an outlook on the development of perturbation generators and methods of altering large-scale flow structures as a potential means for heat and mass transfer control where natural convection is dominant.