As a key nutrient for primary productivity in freshwater ecosystems, the effect of upper cascade reservoirs on the downstream phosphorus (P) loading is subject to an ongoing scientific debate in the Mekong River. To investigate the effects of cascade reservoirs on the forms of P and its bioavailability in surface sediment, two rounds of field research were carried out both in a free-flowing river (Nu River) and in the Upper Mekong River (Lancang River) during winter and summer. Results showed that while the P was trapped with sediments and environmental parameters changed significantly, high relative abundance of bioavailable phosphorus (BioP, generally include Fe-bound P, Al-bound P, and Organic P) in sediment was detected in reservoirs and at near the border between China and Myanmar. The increased Bio-P in reservoirs may be caused by sediments sorting, anaerobic surface sediments, appropriate temperature, longer residence time and algae-nutrient positive feedback loops. Accumulated Bio-P in sediments may elevate the phosphorus release to overlying water and exacerbate eutrophication in reservoirs. Considered the intense anthropogenic phosphorus loading, nutrients enrichment risk in the lower Mekong River should receive more attention in further research.