Monitoring of submerged aquatic vegetation in turbid environment is one of the challenges in remote sensing. In Akkeshi-ko estuary in eastern Hokkaido, water transparency is low, but seagrass leaves approach or reach the water surface during low tide. Thus, using UAVs during the low tide makes it possible to avoid the effects of light attenuation by water and to monitor the seagrass beds dynamics. The present study investigated the areal variation of seagrass beds among month (May to July) and between years (2020 and 2021). Two seagrass species were observed in the study area: Zostera japonica in narrow intertidal zone and Z. marina in more expansive subtidal zone. Among months of the same year, significant increase in cover was observed from spring to summer at shallow area especially for Z. japonica, suggesting a recovery from disturbances by tidal change and ice scour. There was an overall increasing trend between years probably due to lower effect of the disturbances in 2021, and shallow Z. marina exhibited the greatest increase. These results suggest a difference in the rate of horizontal growth among the species, with faster-growing Z. japonica show greater monthly variation and slower-growing Z. marina show greater yearly variation.