Sedimentary organic matter (SOM) in seaweed beds provides an important material foundation for implementing seaweed bed ecosystem services. In this study, SOM samples were collected from the seaweed bed in northern Gouqi Island during the death period in July 2014, growth period in October 2014, and bloom period in May 2015, in accordance with three macroalgal life history stages: germinate and grow, mature and bloom, and decay and die. The sources and variations of the SOM were determined by carbon and nitrogen stable isotope analysis using the molar carbon-to-nitrogen (C/N) ratio and stable isotope composition (δ¹³C and δ¹⁵N) as indicators. The results showed the following. 1) The molar C/N ratios of the SOM varied in the ranges of 5.9–6.6, 6.0–6.9, and 5.4–6.2 in July, October, and the following May, respectively, indicating a typical marine source of SOM from the seaweed bed. 2) The δ¹³C values of the SOM were significantly different at the various water depths in July (–20.3‰ to –17.6‰); however, no significant changes were found in October (–22.3‰ to –21.7‰) or in May of the following year (–21.4‰ to –21.0‰). 3) The δ¹³C values of the SOM showed temporal variations, whereas spatial variations with water depth were found in July. 4) According to the relations among the δ¹³C, δ¹⁵N, and C/N, the SOM was mainly derived from the mixed contribution of phytoplankton and macroalgae in July, and it was attributed to the contribution of phytoplankton in October and the following May. 5) In July, macroalgae, on average, contributed up to 53.71% of the SOM from the seaweed bed, as estimated by the carbon stable isotope mass-balance mixing model. 6) The proportion of macroalgal detritus in the SOM was significantly affected by waves, among the various hydrodynamic factors in the marine environment.