Leaf and rhizome/root biomass from seagrass species Zostera muelleri underwent a 2-year decomposition experiment in the Brisbane Water Estuary, north of Sydney, NSW, Australia. In addition to 16S rRNA gene amplicon analyses for prokaryotic communities associated with the decay seagrass, other response variable included elemental carbon and nitrogen analysis, thermogravimetric analysis, exponential decay rates and a novel dynamic decay model. Seagrass microbiomes during decay (16S) are associated with project/study ERP118498.