The 1999 Kocaeli (Izmit) Earthquake seriously damaged the downtown area of Adapazari, Turkey. The wavefield of the strong ground motions is considered to have been affected by the deep ground structure. A refraction and reflection seismic survey was made to obtain the velocity structure of the profile in the north–south direction across the basin. A 3D subsurface model is presented based on results of the refraction and reflection survey, on data obtained from a gravity survey, and on observations of microseisms and aftershocks. The proposed model shows deep sediment with a steep slope beneath downtown Adapazari. Strong ground motions in the frequency range of 0.1–1.0 Hz propagating in the subsurface model during the Kocaeli Earthquake also were simulated numerically by the 3D finite-difference method. The simulated results show that ground motions in downtown Adapazari were larger than those in the area between downtown and the source fault because the former were significantly amplified by the basin-edge effect.