• Recent McCallum et al., 2012 , Luce et al., 2013 methods added to VFLUX. • Recent methods are tested with non-steady flows, and in 3D heterogeneous media. • Spatial or temporal changes in thermal diffusivity output suggests errors in flux. • Amplitude ratio, or combined amplitude ratio and phase shift methods recommended. Vertical fluid exchange between surface water and groundwater can be estimated using diurnal signals from temperature time series methods based on amplitude ratios ( A r ), phase shifts (Δ ϕ ), or combined use of both ( A r Δ ϕ ). The A r , Δ ϕ , and A r Δ ϕ methods are typically applied in conditions where one or more of their underlying assumptions are violated, and the reliability of the various methods in response to non-ideal conditions is unclear. Additionally, A r Δ ϕ methods offer the ability to estimate thermal diffusivity ( κ e ) without assuming any thermal parameters, although the value of such output has not been broadly tested. The A r , Δ ϕ , and A r Δ ϕ methods are tested under non-steady, 1D flows in sand column experiments, and multi-dimensional flows in heterogeneous media in numerical modeling experiments. Results show that, in non-steady flow conditions, estimated κ e values outside of a plausible range for streambed materials (0.028–0.180 m 2 d −1 ) coincide with time periods with erroneous flux estimates. In heterogeneous media, sudden changes of κ e with depth also coincide with erroneous flux estimates. When (known) fluxes are variable in time, poor identification of Δ ϕ leads to poor flux estimates from Δ ϕ and A r Δ ϕ methods. However, when fluxes are steady, or near zero, A r Δ ϕ methods provide the most accurate flux estimates. This comparison of A r , Δ ϕ and A r Δ ϕ methods under non-ideal conditions provides guidance on their use. In this study, A r Δ ϕ methods have been coded into a new version of VFLUX, allowing users easy access to recent advances in heat tracing.