Groundwater is a primary hydrological reservoir of the Great Lakes Water Basin (GLB), which is an important region to both Canada and US in terms of culture, society and economy. Due to insufficient observations, there is a knowledge gap about groundwater storage variation and its interaction with the Great Lakes. The objective of this study is to examine the detectability of the groundwater storage change within the GLB using the monthly models from the Gravity Recovery And Climate Experiment (GRACE) satellite mission, auxiliary soil moisture, snow and lake (SMSL) data, and predictions from glacial isostatic adjustment (GIA) models. A two-step filtering method is developed to optimize the extraction of GRACE signal. A two dimensional basin window weight function is also introduced to reduce ringing artifacts caused by the band-limited GRACE models in estimating the water storage change within the GLB. The groundwater storage (GWS) as deviation from a reference mean storage is estimated for the period of 2002 to 2009. The average GWS of the GLB clearly show an annual cycle with an amplitude range from 27 to 91 mm in water thickness equivalent (WTE), and a phase range of about two months. The estimated phases of GWS variations have a half year shift with respect to the phase of SMSL water storage variations which show peaks in March and April. The least squares estimation gives a GWS loss trend of from 2.3 to 9.3 km3/yr within the GLB for the period of study. This wide range of the GRACE GWS results is caused largely by the differences of soil moisture and snow storage from different land surface models (LSMs), and to a lesser extent by the GRACE commission and omission errors, and the GIA model error.