To design the foundation of a fixed-type wind turbine, the geotechnical data of the region in different depths below the seafloor must be surveyed using a cone penetration test (CPT). A common methodology to carry out the CPT in shallow water is to use a drillstring to drill a well. Then the drillstring must be anchored and a cone probe is conveyed within the drillstring to survey the undisturbed soil a few meters below the bit. However, during the period the drillstring is anchored in a relative high-current environment, it will be exposed to the vortex-induced vibration (VIV). In this article, we will present the VIV numerical analysis to assess the stress and accumulate fatigue on the drillstring. The simulation was calculated in the frequency domain using commercial software for marine riser analysis used by the Petroleum Industry. We compared two different drillstrings, one composed by Bottom Hole Assembly (BHA) and drill pipe and the other using BHA and heavyweight drill pipe. The VIV results show slightly better performance of the string composed by heavy weight drill pipes.