Abstract We propose that flow distortion within a non-orthogonal CSAT3 sonic anemometer is primarily due to transducer shadowing, which is caused by wakes in the lee of the acoustic transducers impinging on their measurement paths. The dependence of transducer shadowing on sonic path geometry, wind direction and atmospheric stability is investigated with simulations that use surface-layer data from the Horizontal Array Turbulence Study (HATS) field program and canopy roughness-sublayer data from the CHATS (Canopy HATS) field program. We demonstrate the efficacy of correcting the CSAT3 for transducer shadowing with measurements of its flow distortion in the NCAR wind tunnel, combined with 6 months of data collected in the atmospheric surface layer with adjacent CSAT3 and orthogonal ATI-K sonic anemometers at the NCAR Marshall field site. CSAT3 and ATI-K measurements of the variance of vertical velocity $$\sigma _w^2$$ σ w 2 and the vertical flux of sonic temperature agree within 1 % after correction of both sonics for transducer shadowing. Both the simulations of transducer shadowing and the comparison of CSAT3 and ATI-K field data suggest a simple, approximate correction of CSAT3 surface-layer scalar fluxes with an increase on the order of 4–5 %, independent of wind direction and atmospheric stability. We also find that $$\sigma _w/u_*$$ σ w / u ∗ (where $$u_*$$ u ∗ is the friction velocity) and $$r_{uw}$$ r u w (the correlation coefficient) calculated with corrected CSAT3 data are insensitive to wind direction and agree closely with known values of these dimensionless variables for neutral stratification, which is evidence for the efficacy of the correction of the horizontal wind components for transducer shadowing as well.

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