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Results are presented for towing tank experiments of a surface-piercing flat plate with superimposed Stokes wave in order to examine free surface and wave effects on the boundary layer and wake. Measurements with servo wave gauges are made to characterize the Stokes-wave wave field in terms of its two-dimensionality, amplitude, and wavelength. Flow field measurements using stereo particle image velocimetry are used to identify the boundary layer and wake velocities. Particular attention is drawn to the juncture region to resolve the complex and poorly understood secondary flow patterns. Four test cases are presented (1) flat free surface without plate, (2) Stokes-wave without plate, (3) flat free surface with plate, and (4) Stokes-wave with plate; the cases were chosen in order to isolate and identify the performance of the velocimeter system, Stokes-wave flow field, free-surface effects, and combined Stokes-wave and free surface effects, respectively. All cases are conducted at Froude numbers of Fn = 0.4, length-based Reynolds number of Re = 1.64×106, and momentum thickness-based Reynolds number of about Re = 4000. Results show, as expected, that the free surface effects penetrate to a depth slightly greater than the boundary layer thickness and wave effects diminish at roughly one half the wavelength. The juncture region flow was resolved to levels that far exceed previous towing tank experiments, but leave more to be desired. The data and analysis are important, not only from a scientific perspective, but have a practical application with regard to development of turbulence models for computational fluid dynamic techniques.