Information on ongoing climate change impacts on water availability is limited for Asian regions, particularly for Peninsular Malaysia. Annual flash floods are common during peak monsoon seasons, while the dry seasons are hit by droughts, leading to socio-economic stress. This study, for the first time, analyzed the long-term trends (14 years, from 2002 to 2014) in terrestrial water storage and groundwater storage for Peninsular Malaysia, using Gravity Recovery And Climate Experiment data. Results indicate a decline in net terrestrial and groundwater storage over the last decade. Spatially, the northern regions are more affected by droughts, while the southern regions have more flash floods. Groundwater storage trends show strong correlations to the monsoon seasons, indicating that most of the shallow aquifer groundwater is used. Results also indicate that, with proper planning and management, excess monsoon/flash flood water can be stored in water storage structures up to the order of 87 billion liters per year. This can help in dry season water distribution and water transfer projects. Findings from this study can expand the understanding of ongoing climate change impacts on groundwater storage and terrestrial water storage, and can lead to better management of water resources in Peninsular Malaysia.