The application of two methods of analysis to the movement of a tracer through trees, involving 'total counts' or convection-dispersion models, is discussed, particularly in relation to fluctuating flows. A rigorous definition of the 'measured' flow rate obtained with the total counts method is developed. It is shown, from the principle of conservation of mass, that the total counts method provides an estimate of the weighted mean flow over the time period that the tracer is present at the sampling point. The weighting factor is the relative concentration of the tracer as measured at the sampling point. Using results from a tracing experiment on Eucalyptus teretecornis it is shown that the system parameters, diffusivity, porosity and convective flow velocity, are such that the time scale of the weighted mean flow-rate determination is a period of the order of 2 to 3 days. It is also shown that diurnal fluctuations in flow do not introduce significant errors in the estimate of the weighted mean flow estimate. Application of the convection-dispersion model allows these system parameters to be calculated. Although the implications of the use of these methods are discussed in relation to the flow of tracer through tree stems, they are equally valid in any situation in which the 'total counts' method is used.