Elemental ratios (δ13C, δ15N and C/N) and carbon and nitrogen concentrations in macrophytes, sediments and sponges of the hypersaline Al-Kharrar Lagoon (KL), at the centrale of eastern Red Sea coast, were measured to distinguish their sources, pathways and see how they have been influenced by biogeochemical processes and terrestrial inputs. The mangroves and halophytes showed the most depleted δ13C values of –27.07±0.2 ‰ and –28.34±0.4 ‰, respectively, indicating their preferential 12C uptake, similar to C3-photosynthetic plants, except of for the halophytes Atriplex sp. and Suaeda vermiculata which showed δ13C of –14.31±0.6 ‰, similar to C4-plants. Macroalgae were divided into A and B groups based on their δ13C values. The δ13C of macroalgae A averaged of  –15.41±0.4 ‰, whereas macroalgae B and seagrasses showed values of –7.41±0.8 ‰ and –7.98 ‰, suggesting uptake of HCO3– as a source for CO2 during photosynthesis. The δ13C of sponges was –10.7±0.3 ‰, suggesting that macroalgae and seagrasses are their main favouredable diets. Substrates of all these taxa showed δ13C of –15.52±0.8 ‰, suggesting the KL is at present a macroalgae-dominated lagoon. The δ15N in taxa/sediments averaged of 1.68 ‰, suggesting that atmospheric N2-fixation is thea main source of nitrogen in/around the lagoon. The heaviest δ15N (10.58 ‰) of in halophytes growing in algal mats and sabkha is possibly due to denitrification and ammonia evaporation. The macrophytes in the KL showed high C %, N %, and C/N ratios, but this is not indicated in their substrates due possibly to a rapid turnover of dense, hypersaline waters carrying out a considerable partmost of the detached organic materials out into the Red Sea. The δ13C allowed separation of subaerial from aquatic macrophytes, a proxy that could be used when interpreting paleo-leo–, sea level or paleoclimatic changes from the coastal marine sediments.