Eutrophication is a significant threat to surface water biodiversity worldwide, with excessive phosphorus concentrations being among the most common causes. Wetland ditches under these conditions shift from primarily submerged aquatic vegetation to algae or duckweed dominance, leading to excessive shading and anoxic conditions. Phosphorus, from both point (e.g. wastewater treatment works) and diffuse (largely agricultural runoff) sources, is currently the central reason for failure in the majority of surface water bodies in England to meet required water quality guidelines. This study assesses phosphorus storage in the ditch systems at West Sedgemoor, a designated site of special scientific interest. Elevated phosphorus concentrations in sediment was observed across the Moor up to 4220 mg Kg−1, almost 10 times that which may be expected from background levels. The highest concentrations were generally observed at the more intensively farmed sites in the north of the moor, near key inlets and the outlet. Based upon their chemical and physical properties, clear distinction was observed between sites outside and within the Royal Society of the Protection of Birds nature reserve, using principal component analysis. Display omitted •Exceptionally high sediment P concentrations observed e.g. >4000 mg kg−1.•Higher P concentrations observed at the north of the moor, the inlets and outlet.•Principal component analysis distinguished sites by land management approaches.•Higher P concentrations observed near agricultural land compared to nature reserve.•Observations indicate relatively higher P input from agricultural land.