Sediment　organic　matter　(SOM)　is　important　in　the　biogeochemical　cycling　of　carbon,　nutrients,　and　pollutants　in　the　coastal　environment,　which　is　increasingly　disturbed　by　aquaculture　that　is　particularly　intense　in　China.　However,　the　identification　of　aquaculture　signals　in　SOM　is　rather　challenging　in　the　complex　coastal　environment　that　receives　materials　from　a　variety　of　sources.　This　was　studied　in　a　typical　culture　area　of　shellfish　and　algae　in　SE　China　from　July　2019　to　October　2020,　using　a　combination　of　elemental　(OC,　TN,　N/C),　isotopic　(delta　C-13　and　delta　N-15),　spectral　(absorption　spectroscopy　and　fluorescence　EEMs-PARAFAC),　and　statistical　analysis　(principal　component　analysis,　PCA).　All　indices　of　SOM　quantity　and　several　spectral　indices　for　the　SOM　composition　correlated　significantly　with　grain　size,　with　lower　SOM　quantity　and　higher　autochthonous　contribution　in　coarse　sediments.　The　strong　correlations　between　elemental　and　spectral　indices　suggested　that　optical　analysis　could　provide　valuable　indices　for　assessing　the　quantity　of　bulk　organic　matter.　The　comparison　of　SOM　indices　between　different　zones　and　between　different　months　showed　an　overall　limited　influence　of　shellfish　and　laver　culture.　This　indicated　the　sustainability　of　these　types　of　aquaculture　that　require　no　manual　addition　of　feeds　and　thus　are　generally　clean.　The　further　applications　of　end-member　mixing　analysis　using　the　IsoSource　program　and　PCA　were　more　sensitive,　which　identified　the　removal　of　SOM　by　shellfish　in　the　growing　season　and　the　contribution　from　shellfish　residuals　after　the　harvest　and　the　cultured　laver　at　some　locations.　Overall,　our　results　have　implications　for　a　better　understanding　of　the　biogeochemical　processes　and　ecosystem　sustainability　in　the　coastal　environment　under　intense　aquaculture　activities.