This is a dataset of organic carbon, nitrogen, and phosphorus content from the Olifants estuary. The study was designed to investigate drivers of variability at different spatial scales and across the salt marsh-seagrass ecotone. Samples were collected in March 2023 from three selected sites (upper, middle, and lower) in the estuary. Each site featured three transects, extending from the salt marsh vegetation of mixed species through the Zostera capensis seagrass meadows towards the water. Sediment cores were taken to a depth of 50 cm, but only the top 0-5 cm section was analyzed. Carbon and nitrogen content were measured using an Elementar Vario EL Cube Elemental CHNS Analyzer, while phosphorus was determined by ICP at Central Analytical Facilities (Stellenbosch University). Sampling site GPS coordinates Upper 31°39'45.27"S, 18°11'42.40"E Middle 31°40'56.46"S, 18°12'3.72"E Lower 31°41'39.85"S, 18°11'15.95"E File description CHNS_Dataset_SM&INT.xlsx: Data for intermediate sample measurements including percent organic carbon content and and percent nitrogen content for all sites ICP_Data_INT.xlsx: Data for Phosphorus content and other related measurements for the upper site.