We have studied the effects of local topography and canopy structure on turbulent flux measurements at a site located in mountainous terrain within a subalpine, coniferous forest. Our primary aim was to determine whether the complex terrain of the site affects the accuracy of eddy flux measurements from a practical perspective. We observed displacement heights, roughness lengths, spectral peaks, turbulent length scales, and profiles of turbulent intensities that were comparable in magnitude and pattern to those reported for forest canopies in simpler terrain. We conclude that in many of these statistical measures, the local canopy exerts considerably more influence than does topographical complexity. Lack of vertical flux divergence and modeling suggests that the flux footprints for the site are within the standards acceptable for the application of flux statistics. We investigated three different methods of coordinate rotation: double rotation (DR), triple rotation (TR), and planar-fit rotation (PF). Significant variability in rotation angles at low wind speeds was encountered with the commonly used DR and TR methods, as opposed to the PF method, causing some overestimation of the fluxes. However, these differences in fluxes were small when applied to large datasets involving sensible heat and CO2 fluxes. We observed evidence of frequent drainage flows near the ground during stable, stratified conditions at night. Concurrent with the appearance of these flows, we observed a positive bias in the mean vertical wind speed, presumably due to subtle topographic variations inducing a flow convergence below the measurement sensors. In the presence of such drainage flows, advection of scalars and non-zero bias in the mean vertical wind speed can complicate closure of the mass conservation budget at the site.