In order to provide technical support for in-situ long-term observation researches of sediment-water interface fluxes, realization and application of the aquatic eddy correlation technique were systematically arranged. The development history and technical characteristics of the aquatic eddy correlation technique were reviewed. The technical methodology was introduced from the aspects of theoretical basis, system construction and data processings and the application direction and current challenges of this technique were summarized. The aquatic eddy correlation technique could be applied to different sediment types while does not interfere with their structure and it has the characteristics of large measurement footprint and high resolution. Therefore, this technique is suitable for sediment-water interface flux observation in various environments such as rivers, lakes, reservoirs, bays and deep oceans, which could further provide supports for studies on water environment restoration, ecosystem metabolism assessment and hyporheic exchange.