Zostera muelleri is an abundant seagrass species distributed through intertidal and shallow subtidal waters on the subtropical coasts of Australia. The vertical distribution of Zostera is likely defined by tidal influences, particularly desiccation and light reduction stresses. These stresses were expected to affect the flowering of Z. muelleri; however, it is difficult to quantify the effects of tidal inundation with field studies due to multiple confounding environmental factors affecting flowering (e.g., water temperature, herbivory, nutrients). A laboratory aquarium experiment compared the effects of two levels of tidal height (intertidal and subtidal) and light intensity (shaded and unshaded) on flowering timing, abundance, the ratio between flowering shoots and vegetative shoots, the morphology and duration of flower development. The earliest and greatest flowering intensity was recorded in the subtidal-unshaded group, with no flowers observed in the intertidal-shaded group. Notably, the peak flowering time was the same across shaded and unshaded treatments. Shading prolonged the timing of the first flowering and reduced the density of flowering shoots and spathes, while tidal inundation had a more significant effect on the density of flowering shoots and the density of spathes. Results showed that Z. muelleri could flower under low light conditions or tidal stress but not when exposed to both stresses simultaneously in a laboratory ‘nursery setting’. Therefore, applying subtidal-unshaded conditions appears to be beneficial for seagrass nurseries aimed at improved flower abundance despite the plants previously being collected from and adapted to intertidal meadows. Further studies that explore the suitable conditions for triggering and optimising the flowering will be beneficial in designing cost-effective seagrass nurseries.