A field experiment is described in which diapycnal diffusivity is estimated by direct and indirect methods in Swan river estuary, Perth, Western Australia. The microstructure profiles were collected in a narrow and straight part of this estuary using a portable flux profiler (PFP). The profiles were segmented into stationary parts and the rate of vertical eddy diffusivity was estimated for the segments within the pycnocline. The direct measurement showed that instantaneous flux could be positive or negative with a low net rate of vertical eddy diffusivity for mass of about 6.5 × 10−8 m2 s−1. All the indirect methods overestimated this rate. However, within the indirect methods, the method of Osborn yielded the poorest estimate while the method of Osborn and Cox gave the closest estimate.