A comparison of groundwater velocity in heterogeneous aquifers estimated from hydraulic methods, heat and solute tracers was made using numerical simulations. Aquifer heterogeneity was described by geostatistical properties of the Borden, Cape Cod, North Bay, and MADE aquifers. Both heat and solute tracers displayed little systematic under- or over-estimation in velocity relative to a hydraulic control. The worst cases were under-estimates of 6.63% for solute and 2.13% for the heat tracer. Both under- and over-estimation of velocity from the heat tracer relative to the solute tracer occurred. Differences between the estimates from the tracer methods increased as the mean velocity decreased, owing to differences in rates of molecular diffusion and thermal conduction. The variance in estimated velocity using all methods increased as the variance in log-hydraulic conductivity (K) and correlation length scales increased. The variance in velocity for each scenario was remarkably small when compared to σ2ln(K) for all methods tested. The largest variability identified was for the solute tracer where 95% of velocity estimates ranged by a factor of 19 in simulations where 95% of the K values varied by almost four orders of magnitude. For the same K-fields, this range was a factor of 11 for the heat tracer. The variance in estimated velocity was always lowest when using heat as a tracer. The study results suggest that a solute tracer will provide more understanding about the variance in velocity caused by aquifer heterogeneity and a heat tracer provides a better approximation of the mean velocity.