Harmful algal blooms(HABs) can elicit several negative effects on aquatic environment(such as depleting the oxygen, blocking the sunlight, destroying the habitats of organisms) and life health(including poisoning/killing marine mammals, birds and human). Among the various control strategies for HABs(physical manipulation needs lots of manpower and expensive equipment, chemicals treatment has some toxic byproduct and high residual, microbial agents only has limited in laboratory research), the coagulation-flocculation of HAB species by modified clay(MC) has been proven to be an effective, lowcost and environmentally friendly method that has been widely applied in the field, particularly in eastern Asia. In order to examine the long-term effects of MC treatment, this study investigated the alternations in seawater of Skeletonema costatum, a high biomass dominant HAB species along the Chinese coast, by comparing the degradation of S. costatum detritus(A1) with the application of MC treatment(A2) and MC treatment in sediment condition(A3). The low dosage of 0.25 g/L MC could efficiently remove 4×108 cells/L of S. costatum cells within 3.5 h(approximately 97% removal). In addition, the results showed that both inorganic and organic nutrients were effectively reduced from seawater by MC particles. Compared to the total nitrogen(TN) and total phosphorus(TP) concentrations in A1 seawater, 44% of TN and 93% of TP in A2 seawater, as well as 72% of TN and 93% of TP in A3 seawater were removed during the onemonth incubation period. Simultaneously, 64% of DISi in A2 and 44% of DISi in A3 significantly decreased( P <0.001). This study demonstrated that MC treatment was able to significantly increase the downward flux of nutrients and delay the release velocity of inorganic nutrient from MC-algae matrix into the overlying seawater, particularly within sediment environment. Among the various (HABs) can elicit several negative effects on aquatic environment (such as depleting the oxygen, blocking the sunlight, destroying the habitats of organisms) and life health (including poisoning / killing marine mammals, birds and human). control strategies for HABs (physical manipulation needs lots of manpower and expensive equipment, chemicals treatment has some toxic byproduct and high residual, microbial agents only has limited in laboratory research), the coagulation-flocculation of HAB species by modified clay (MC) has been proven to be an effective, lowcost and environmentally friendly method that has been greatly applied in the field, particularly in eastern Asia. In order to examine the long-term effects of MC treatment, this study investigated the alternations in seawater of Skeletonema costatum, a high biomass dominant HAB species along the Chinese coast, by comparing the degradation of S. costatum detritus (A1) with the application of MC treatm (A2) and MC treatment in sediment condition (A3). The low dosage of 0.25 g / L MC could efficiently remove 4 × 108 cells / L of S. costatum cells within 3.5 h (approximately 97% removal) Compared to the total nitrogen (TN) and total phosphorus (TP) concentrations in A1 seawater, 44% of TN and 93% of TP in A2 seawater, Simultaneously, 64% of DISi in A2 and 44% of DISi in A3 significantly decreased (P <0.001). This study demonstrates that 72% of TN and 93% of TP in A3 seawater were removed during the one-month incubation period. MC treatment was able to significantly increase the downward flux of nutrients and delay the release velocity of inorganic nutrient from MC-algae matrix into the overlying seawater, particularly within sediment environment.