It depends on which type of the organism and environmental samples you want to focus. In my recent publication (there is a share link to this publication: https://authors.elsevier.com/a/1YMzP,XRNLZ38-) I investigated one common plant in the estuary zone as well as in the shallow bay of brackish Baltic Sea. I focused on carbon stable isotope composition and if you consider studying organic matter I usually recommend to investigate also the carbon isotope of Dissolved Inorganic Carbon (DIC) as main variables which influence the values of the stable isotopic composition of plant organic matter. In the case of carbon and nitrogen isotope composition of the aquatic plant, there is very good publication: https://onlinelibrary.wiley.com/doi/abs/10.1111/fwb.12996. Also, I can recommend very good publication about estuary study of stable carbon and nitrogen isotopic composition of the different type of plants including phytoplankton study https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2002.47.3.0713. As an inorganic part of carbon dynamic, I recommend to focus on carbonates study (formed by different animals which create shells or precipitated by plants during photosynthesis process or those of allochthonous origin if you can divide it ). For carbonates stable carbon and oxygen isotope compositions is also good to know the carbon stable isotope composition of DIC and stable oxygen isotope composition of water. But if you want to focus mainly on carbon dynamics in an estuary system, in my opinion, you should also investigate the small form of organic matter components such Dissolved Organic Matter (DOC) in relation to DIC and other environmental variables.