Flow instabilities leading to the formation of streamwise vortices in a natural convection boundary layer over a heated inclined plate submerged in a water tank are manipulated using spanwise arrays of surface-mounted heating elements. The flow over the plate is driven by a two-ply surface heater comprised of a uniform, constant- heat flux heater and a mosaic of 32 × 12 individually controlled heating elements that are used as control actuators. Surface temperature distributions are measured using liquid crystal thermography and the fluid velocity in cross-stream planes is measured using particle image velocimetry (PIV). Time-invariant spanwise-periodic excitation over a range of spanwise wavelengths leads to the formation of arrays of counter-rotating streamwise vortex pairs and to substantial modification of the surface temperature and heat transfer. The increase in surface heat transfer is accompanied by increased entrainment of ambient fluid and, as a consequence, higher streamwise flowrate. Subsequent spanwise-periodic merging of groups of vortices farther downstream retards the streamwise increase of the surface heat transfer rate. Finally, the suppression of small-amplitude spanwise disturbances by linear cancellation is demonstrated.