We surveyed two seagrass beds and two mudflats in each of six coastal sites in England (Holy Island, Blackwater, Thames, Chichester, Plymouth, Morecambe) between December 2024 and March 2025 to characterise national differences in denitrification rates and their relationship with potential drivers. A key ecosystem service in coastal systems is the remediation of nutrient pollution through sediment burial, vegetative uptake and microbial processing. Denitrification is a facultative anaerobic process where microbial activity transforms nitrate (NO3-), which in high concentrations can be environmentally harmful, into the environmentally benign dinitrogen gas (N2). Denitrification's magnitude is considered particularly important in saltmarsh systems compared to other habitats, although an intermediate product, nitrous oxide (N2O), can also be given off and contribute to climate change. This data accompanies the technical report "Denitrification dynamics and relationships with potential drivers across English saltmarshes, seagrass beds, and mudflats: Capturing national variation in space and time" Full details about this dataset can be found at https://doi.org/10.5285/ea9811f4-5856-4a7e-bbe6-dcea9c115ea2