The outbreak and scale of harmful algal blooms (HABs) have been on the rise in recent years, mainly attributed to the effects of worsening seawater eutrophication and climatechange-related temperature increases. Yet, current approaches for detecting HABs fail to meet the requirements of rapid qualification and on-site quantification of the algae species and early warning of the outbreaks. Herein, an electrochemical biosensor based on In 2 O 3 /NC/Au NP nanomaterials was developed for the dynamic detection of Skeletonema costatum (S. costatum), one of the typical HABs. Specifically, the biosensor demonstrated a lower limit of detection (LOD, 671 fg/μL or 3528 cells/L) and had been confirmed to be accurate and reliable when compared to droplet digital PCR (ddPCR) and traditional microscope techniques. Moreover, for actual sample analysis, the concentrations of S. costatum were determined as 3.8 × 10 3 to 2.1 × 10 5 cells/L by the biosensor, which demonstrated a lower risk of S. costatum bloom outbreak in the sampling region and was consistent with the standard survey method. Therefore, the biosensor has great potential in the early stage qualitative analysis and on-site quantification of S. costatum and serves as an ideal warning technology of HAB outbreaks.