Many methods of passive flow control rely on changes to surface morphology. Roughening surfaces to induce boundary layer transition to turbulence and in turn delay separation is a powerful approach to lowering drag on bluff bodies. While the influence in broad terms of how roughness and other means of passive flow control to delay separation on bluff bodies is known, basic mechanisms are not well understood. Of particular interest for the current work is understanding the role of surface dimpling on boundary layers. A computational approach is employed and the study has two main goals. The first is to understand and advance the numerical methodology utilized for the computations. The second is to shed some light on the details of how surface dimples distort boundary layers and cause transition to turbulence. Simulations are performed of the flow over a simplified configuration: the flow of a boundary layer over a dimpled flat plate. The flow is modeled using an immersed boundary as a representation of the dimpled surface along with direct numerical simulation of the Navier-Stokes equations. The dimple geometry used is fixed and is that of a spherical depression in the flat plate with a depth-to-diameter ratio of 0.1. The dimples are arranged in staggered rows separated by spacing of the center of the bottom of the dimples by one diameter in both the spanwise and streamwise dimensions. The simulations are conducted for both two and three staggered rows of dimples. Flow variables are normalized at the inlet by the dimple depth and the Reynolds number is specified as 4000 (based on freestream velocity and inlet boundary layer thickness). First and second order statistics show the turbulent boundary layers correlate well to channel flow and flow of a zero pressure gradient flat plate boundary layers in the viscous sublayer and the buffer layer, but deviates further away from the wall. The forcing of transition to turbulence by the dimples is unlike the transition caused by a naturally transitioning flow, a small perturbation such as trip tape in experimental flows, or noise in the inlet condition for computational flows.