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Many coastal ecosystems have a high carbon (C) and nitrogen (N) accumulation capacity. Extractable C and N have been shown to be useful indicators to assess changes in soil C and N in terrestrial systems but have not been widely used in coastal habitats. Here, we quantified cold and hot water extractable organic C (cweC, hweC) and N (cweN, hweN) and determined specific ultraviolet absorbance (SUVA 254) to evaluate how water extractable C and N concentration and chemistry change along the transition from mangrove (vegetated) to tidal flat (non-vegetated) and with sediment depth. Sediment cores (20 cm depth) were collected along transects in a muddy (29–46 % clay + silt, Snells Beach) and sandy (8–11% clay + silt, Hobson Bay) estuary in the Auckland region, New Zealand. Cold water exactable C and N concentrations were similar in the muddy and sandy estuary (7–173 μg C g−1 soil; 1–32 μg N g−1 soil). However, cweC and cweN made up a larger proportion of sediment C and N concentration at the sandy estuary. The hweC and hweN concentrations were significantly higher in the muddy (240–2440 μg C g−1 soil; 25–244 μg N g−1 soil) than sandy estuary (50–960 μg C g−1 soil; 6–119 μg N g−1 soil) suggesting a higher release of C and N from the muddy estuary with organic matter rich sediments. Habitat had a strong effect at both sites with extractable C and N concentrations being higher in mangroves compared to tidal flat. The C:N ratios and SUVA 254 values of cweC tended to be lower than hweC across all habitats in both estuaries, suggesting a higher proportion of algal-derived organic matter and a lower proportion of aromatic molecules. Our findings demonstrate that water extractable C and N provide valuable insights into the quality and drivers of C and N in coastal habitats. • Extractable carbon and nitrogen in mangrove and tidal flat habitats were quantified. • High spatial variation in extractable C and N content and sediment characteristics. • Habitat effect - lower extractable C and N content in tidal flats than mangroves. • Sediment C and N content were key predictors of water extractable C and N. [ABSTRACT FROM AUTHOR]