The total amount and morphology of nitrogen and phosphorus in sediments have important environmental significance. The study of the ecological risk assessment of nitrogen and phosphorus in sediments is important to understand the environmental quality of water body in the basin. In this study, taking the Futunxi Basin of Fujian Province as an example, the single factor index and bioavailability coefficient method were used to evaluate the ecological risk of nitrogen and phosphorus in the sediments, and reveal the spatial change and environmental significance of the nitrogen and phosphorus forms. The results showed that different morphological components of the bio-available nitrogen were distributed as organic sulfide bound nitrogen (SOEF-N) iron-manganese oxidized nitrogen (SAEF-N) weak acid leached nitrogen (WAEF-N) ion exchange nitrogen (IEF-N). The inorganic phosphorus included the highest proportion of metal oxide bound phosphorus (NaOH-P), followed by calcium bound phosphorus (HCl-P). The proportion of reduced phosphorus (BD-P) was even lower, and the proportion of weakly adsorbed phosphorus (NH4Cl-P) was the lowest. The results of single factor pollution index showed that the sediment nitrogen in the study area mainly caused moderate pollution and phosphorus mainly caused light pollution. By contrast, the results of the bioavailability index method indicated that nitrogen mainly caused light pollution, and phosphorus mainly caused clean pollution in sediments. Combined with the characteristics of social economy and environment in the study area, it can be inferred that the bioavailability index method based on comprehensive evaluation of total amount and morphology can better characterize the spatial change and ecological risk of nitrogen and phosphorus in sediments.