Three-dimensional effects due to rotation which decrease the accuracy of predicting the wind turbine aerodynamic performance, are correlated with coherent structures near the blade roots, specifically with the flow separation. This study aims to give an insight into the complex coherent structures and the 3D rotational effects on the flow over spinners of horizontal axis wind turbines. The flow fields for the identification of the coherent structures and the 3D rotational effects are obtained by solving the Reynolds-averaged Navier-Stokes equations. The complex coherent structures, dominated by viscous shear layers are identified in this study by using various vortex detection methods. The coherent structures near the blade roots of the baseline wind turbine include helical root vortices, trailing edge vortices, flow separation with significant radial flows, von Kármán vortex streets, pairs of counter-rotating base vortices, horseshoe vortices, and a low-speed nacelle wake. The correlation between the helical root vortex and the blade-bound circulation is verified. The dominant sources responsible for the 3D rotational effect on attached and detached boundary layers are estimated by means of order of magnitude analysis. The 3D rotational effect on the baseline wind turbine results in lift augmentation, drag reduction, and significant radial flows in the flow separation region. The significant radial velocity components in the flow separation region are predictable, and substantially driven by the centrifugal acceleration. The Coriolis acceleration in the chordwise direction, induced by these significant radial velocity components in the bottom of the detached boundary layer, is balanced by a pressure gradient in the chordwise direction. This pressure gradient in the chordwise direction over the rotating blade agree well with the analytical expression derived in this study. The separation point is determined accurately in this study by a new criterion based on skin friction coefficients. The limited shift of separation points on the rotating blade, either towards the trailing edge or leading edge, indicates different effects due to rotation on the attached and detached boundary layers.