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It is known that asynchronous temporal variations in local populations can contribute to the stability of metapopulations. However, studies evaluating the hierarchical organization of multiple spatial scales are rare for continuous marine landscapes, especially for marine vegetation such as seagrass beds. In this study, long‐term observation (26 yr) of temporal changes and nested spatial analyses were combined for an extensive seagrass meadow in Tokyo Bay, Japan, using remote sensing and geographic information system technologies. We examined how the dynamics at the whole‐bed scale (~1 km²) are related to those at a local scale (0.04 km²), and investigated the relationship between the seagrass dynamics and long‐term changes in environmental conditions using data on oceanography, water quality, and sediment dynamics. The seagrass bed size fluctuated between a maximum of 1.28 km² (in 1987 …