Seagrass flowering is essential to maintain genetic diversity and the meadow’s resilience. In patchy intertidal meadows, flowering is highly variable; however, the reason for the variation is still unknown. Three monthly 100 m transect surveys were conducted in two Zostera muelleri meadows in subtropical Australia over two consecutive flowering seasons (July-December). Along each transect, the presence of flowering and spathes density (seed-bearing structure), plant cover, and depth were measured every 10 m. The peak flowering was observed during mid-Austral spring. The flowering presence is correlated to plant cover, and spatiotemporal variability of spathe density is defined by plant cover, depth, and their interaction. The plant cover has a significant effect in both models, suggesting that the plant’s flowering potential is related to the number of individuals occupied in the area. The effect of depth was not significant, suggesting that the flower production in an intertidal meadow may not substantially affect by depth. Spathe density was not significantly differed among intertidal depth categories during the peak flowering. Flower production in an intertidal meadow is influenced by plant cover but not intertidal depth. The optimum flowering harvesting times and density of spathes that can be harvested are important for seed-based restoration.