Abstract: As a major trans-basin water transfer project, water-quality safety of the Middle Route Main Canal in the South-to-North Water Diversion Project is of paramount importance． In this study surface sediment and water samples were collected from 14 siltation zones along the canal, to analyze water physicochemical parameters and sediment nutrient contents． Six phosphorus forms were characterized, release potential of endophytic phosphorus was evaluated, and the process of phosphorus deposition was examined． Algae were found to absorb phosphorus from water, to deposit it into sediments upon death, interacting with geochemical processes to drive phosphorus accumulation in sediments． This would result in a phosphorus-limited state in the canal water (average N/P molar ratio of 1203.2), with total phosphorus in sediments predominantly consisting of organic phosphorus and iron-bound phosphorus, and bioavailable phosphorus accounting for 65.8%． Spatially, phosphorus levels showed a trend of higher concentrations in the middle and upper reaches and lower concentrations downstream． Single-factor pollution indices indicate that most monitoring points were at clean or normal levels, while the bioavailable phosphorus index revealed moderate to severe enrichment at multiple points in the middle and upper reaches, indicating high release potential of phosphorus in sediments． To implement water quality regulation, it is recommended to interface redox regulation and calcium-phosphorus transformation, to effectively ensure water quality safety at the Middle Route Main Canal of the South-to-North Water Diversion Project．