•FAO-56 dual crop coefficients (Kcb, Ke, Ks) are used in many agricultural water models.•Kcb, Ke, and Ks are difficult to independently determine.•We determined Kcb, Ke, and Ks by re-analyzing eddy covariance (EC) data.•Method can be used to re-assess existing EC datasets to constrain Kcb, Ke, and Ks. Current approaches to scheduling crop irrigation using reference evapotranspiration (ET0) recommend using a dual-coefficient approach using basal (Kcb) and soil (Ke) coefficients along with a stress coefficient (Ks) to model crop evapotranspiration (ETc), e.g. ETc=(Ks*Kcb+Ke)*ET0. However, determining Ks, Kcb, and Ke from the combined evapotranspiration (ET) is challenging, particularly for Ke, and a new method is needed to more rapidly determine crop coefficients for novel cultivars and cultivation practices. In this study, we partition eddy covariance ET observations into evaporation (E) and transpiration (T) components using correlation structure analysis of high frequency (10–20Hz) observations of carbon dioxide and water vapor (Scanlon and Sahu, 2008) at three irrigated agricultural sites. These include a C4 photosynthetic-pathway species (sugarcane—Sacharum officinarum L.) and a C3 pathway species (peach—Prunus persica) under sub-surface drip and furrow irrigation, respectively. Both sites showed high overall Kc consistent with their height (>4m). The results showed differences in Ke, with the sub-surface drip-irrigated sugarcane having a low Ke (0.1). There was no significant relationship (r2<0.05) between root zone soil volumetric water content (VWC) in sugarcane and observed Kcb*Ks, indicating that there was no stress (Ks=1), while the peach orchard showed mid-season declines in Kcb*Ks when VWC declined below 0.2. Partitioning of Kc into Kcb and Ke resulted in a better regression (r2=0.43) between the Normalized Differential Vegetation Index (NDVI) and Kcb in sugarcane than between NDVI and Kc (r2=0.11). The results indicate the potential for correlation structure flux partitioning to improve crop ET coefficient determination by improved use of eddy covariance observations compared to traditional approaches of lysimeters and microlysimeters and sap flow observations to determine Kc, Ke, Ks, and Kcb.