Seagrass beds are among the most productive and ecologically valuable coastal ecosystems. However, temperate nearshore seagrass beds exposed to urban stressors remain understudied. From 2020 to 2024, this study investigated seagrass communities, environmental factors, and benthic macrofauna in Qingdao’s coastal bays (Qingdao Bay, Huiquan Bay and Tangdao Bay) using field sampling and remote sensing. Redundancy analysis (RDA), Spearman correlation, and PERMANOVA were applied to clarify the ecological response relationships among these components. Results revealed significant spatiotemporal variations: Qingdao Bay experienced severe degradation with an 88% decline in belowground biomass. Huiquan Bay showed shoot height increases but ecological instability, while Tangdao Bay maintained relatively stable conditions. Mollusks dominated Qingdao Bay (67.4%), whereas annelids were prevalent in Huiquan Bay (51.8%) and Tangdao Bay (69.6%). Tangdao Bay supported the most complex and stable benthic communities. Water depth acted as a stressor to seagrass growth, while the role of dissolved oxygen and salinity was complex, exhibiting context-dependent relationships with seagrass parameters. Dissolved inorganic nitrogen and reactive phosphate were shared positive drivers for both seagrasses and macrofauna. This study conclusively links specific environmental drivers to seagrass ecosystem dynamics, delivering essential insights for effective ecological management and restoration strategies.