Zostera muelleri is a dominant seagrass species that distributed widely in intertidal and subtidal waters in subtropical coasts of Australia. Flowering of Zostera is likely to be influenced by environmental stresses associated with tidal fluctuations and light limitation. An aquaria experiment was designed to test two levels of tidal flux (i.e., intertidal and subtidal) and light (i.e., shaded and unshaded) variations on the flowering metrics (1) number of days to first flowering, (2) number of days to peak flowering, (3) the density of spathes, (4) percentage of flowering shoots, (5) height of flowering shoot, (6) number of spathes per flowering shoot and (7) the duration of flower maturity over 24 weeks. The earliest and highest intensity of flowering was recorded in subtidal-unshaded group, with no flowers observed in the intertidal shaded group. Tidal variation had a pronounced effect on the flowering metrics 1, 3, 4 and 5 and the shading significantly effect on the flowering metrics 1 and 3. Results showed that if plants exposed to both tidal variation and light limitation stressors, plant’s flowering is absent or reduced. Understanding flowering variability is critical to understanding seagrass meadow resilience and facilitating restoration when reestablishment is led by sexual reproduction.