This paper evaluates four methods to obtain accurate averaged flux estimates under conditions of non-stationary turbulence. In Part I (Van Kesteren et al., 2012), we introduced and evaluated these four combined methods for 30-min averaging intervals, notably the flux-variance method, the Bowen-variance method, the structure-parameter method, and the energy-balance method. The aim of this paper, Part II, is to validate the accuracy of the 1-min flux estimates of the CO2 flux, FCO2, and the evapotranspiration/latent-heat flux, LvE. Furthermore, we use the 1-min fluxes to investigate flux and vegetation responses under conditions of non-stationary turbulence. Using several validation methods, we show that both the eddy-covariance method and the energy-balance method are unsuitable for estimating fluxes over 1-min averaging intervals. The three other combined methods are more successful in determining 1-min fluxes. The random error is approximately half that of the eddy-covariance method, but still some issues limit the success. The Bowen-variance method has a +0.09 systematic error and moreover, 30% of the data had to be omitted, because the method requires more stringent conditions. Furthermore, the flux-variance method has a -0.15 systematic error. The structure-parameter method performs best of all methods and accurately resolves 1-min fluxes. With this method, we do a final validation with a different data set and show that also under dry conditions the method accurately resolves FCO2, although LE was more difficult to resolve. In the last part, the structure-parameter method is successfully applied under conditions of non-stationary turbulence. We show that LvE and FCO2 have a different step response upon abrupt changes in solar radiation, because different processes drive these fluxes. Also, we observe a 2-min time lag between solar radiation and 1-min fluxes and show the relevance of taking this into account for determining light-response curves of the plants for both 1-min and 30-min averaging intervals. Furthermore, we show the relevance of 1-min fluxes for studying the light-response curves of plants for conditions with different temperature and humidity. Finally, we show that accurate estimates of 1-min averaged canopy resistances can be determined via the resistance expressions for sensible heat and LvE. As such, we show that vegetation can indeed modify its canopy resistance significantly within several minutes. (c) 2013 Elsevier B.V. All rights reserved.