Transient type canopy chambers are still the only currently available practical solution for rapid screening of gas-exchange in agricultural fields. The technique has been criticized for its effect on canopy microclimate during measurement which affects the transport regime and regulation of plant gas-exchange. Field studies in which the technique has been compared against independent methods are still fragmentary. The aims of this study were to quantify the changes of the physical environment during chamber placement, to determine optimum flux measuring windows, to compare three flux-calculation procedures, and to test the performance of the method against independent measurements of sap-flow. Two wheat experiments were conducted for these purposes under German temperate climate conditions. Leaf transpiration and sap-flow remained relatively constant during the first 120s after chamber deployment, but changed considerably afterwards. Canopy H2O fluxes could thus be inferred from concentration measurement series during this interval. A saturation function, previously not mentioned in the literature, was compared against the commonly used constant and quadratic regression methods and identified as the most suitable method for calculating vapor fluxes. The study reconfirmed that small proportional changes of CO2 concentrations during the calculation interval facilitate the application of the frequently applied quadratic regression method for calculating CO2 fluxes. Sap-flow, leaf and canopy gas-exchange were severely perturbed after chamber removal. Revisiting times of same sample locations need to be planned accordingly. The study confirms that the transient chamber technique can be applied for determining canopy gas-exchange, provided that characteristic time intervals within concentration measuring series are determined and their non-linearity tested to establish appropriate flux calculation procedures.