Difficulties in accurately calculating evapotranspiration (ET) in wetlands can lead to inaccurate water balances—information important for many compensatory mitigation projects. Simple meteorological methods or off-site ET data often are used to estimate ET, but these approaches do not include potentially important site-specific factors such as plant community, root-zone water levels, and soil properties. The objective of this study was to compare a commonly used meteorological estimate of potential evapotranspiration (PET) with direct measurements of ET (lysimeters and water-table fluctuations) and small-scale root-zone geochemistry in a natural and constructed wetland system. Unlike what has been commonly noted, the results of the study demonstrated that the commonly used Penman combination method of estimating PET underestimated the ET that was measured directly in the natural wetland over most of the growing season. This result is likely due to surface heterogeneity and related roughness effects not included in the simple PET estimate. The meteorological method more closely approximated season-long measured ET rates in the constructed wetland but may overestimate the ET rate late in the growing season. ET rates also were temporally variable in wetlands over a range of time scales because they can be influenced by the relation of the water table to the root zone and the timing of plant senescence. Small-scale geochemical sampling of the shallow root zone was able to provide an independent evaluation of ET rates, supporting the identification of higher ET rates in the natural wetlands and differences in temporal ET rates due to the timing of senescence. These discrepancies illustrate potential problems with extrapolating off-site estimates of ET or single measurements of ET from a site over space or time.