Flow past a circular cylinder mounted on a flat plate normal to the flow direction is numerically simulated. Three-dimensional mass and momentum conservation equations are solved to obtain the detailed spatio-temporal dynamics of wake vortices revealed through the velocity and pressure data. Particular attention is focused on the junction between the flat plate and the cylindrical cross-section, which is well known to be a rich source of three-dimensional vortical structures. The wake-boundary layer interaction region generates necklace vortices, which are popularly known as horseshoe vortices. The effect of spanwise height (H/D) of the cylinder on these vortices and their unsteady wake characteristics are investigated. The forces acting on the cylinder and the Strouhal periodicities are validated for Re=200, apart from presenting qualitative features, such as streamlines and vorticity contours. The aspect ratio of the cylinder is found to have predominant influence on the primary and secondary vortex structures. Streakline visualization is developed to study the spatio-temporal dynamics of interaction between the wake and the boundary-layer. An assessment of the two types of boundary conditions, viz., free-slip and no-slip (the latter due to bed friction) are investigated. Vortex shedding is found to be completely suppressed for smaller aspect ratios (H/D)≤1.0, with a stabilized flow pattern in the aft of the cylinder, while it persists for H/D>1.0. Copyright © Taylor & Francis Group, LLC.