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The Marine Monitoring Program (MMP) undertaken in the Great Barrier Reef (GBR) lagoon, assesses the long-term effectiveness of the Australian and Queensland Government's Reef Water Quality Protection Plan (Reef Plan). The MMP, established in 2005, is a critical component in the paddock to reef monitoring modelling and reporting program (P2R) that tracks changes in regional water quality and its impact on the GBR as land management practices are improved across Reef catchments. The inshore seagrass component of the MMP assessed seagrass abundance (per cent cover), community structure, relative meadow extent, reproductive health, and nutrient status from inshore seagrass meadows at 29 locations throughout the GBR. Sites were predominately lower littoral (only exposed to air at the lowest of low tides), hereafter referred to as intertidal, although four locations also included shallow subtidal meadows. Each of the Natural Resource Management regions (Cape York, Wet Tropics, Burdekin, Mackay Whitsunday, Fitzroy and Burnett Mary) were represented, including each of the major seagrass habitat types where possible (estuarine, coastal, reef, subtidal). Environmental pressures are also recorded including within-canopy water temperature, canopy light, sediment composition as well as macroalgae and epiphyte abundance, further data obtained from the Australian Bureau of Meteorology and from the MMP inshore water quality subprogram.