Land use and land cover changes (LULCC) associated with urbanization affect watershed functions and services through fundamental alteration of biogeochemical cycles. Quantifying the potential changes in water, carbon, and energy due to urbanization helps sustainable city planning and integrated watershed management. We hypothesize that ‘impacts of urbanization do not create equal’. We conducted two case studies in the US and China at watershed to national scales to show how urbanization affect watershed hydrology, meteorology, and Gross Primary Productivity (GPP). We used both empirical data and ecohydrological models including WaSSI, SWAT, and MIKE SHE. We used stepwise regression and geographically weighted regression models to assess the variable impacts of urbanization on watershed water and carbon balances across a large disturbance and climatic gradient. We show that LULCC may overwhelm the impacts of climate warming on hydrology and urban microclimate (Urban Heat Island and Urban Dry Island) in the humid southern China. We found that the impacts of urbanization on both water yield and GPP are more pronounced in the area with high precipitation and forest covers. The magnitude of changes in ecosystem functions were influenced by many factors such as the background climate (high precipitation vs. low precipitation), previous land use and cover types and land use and cover changes, and the magnitude of urbanization (change in % impervious surface). We conclude that effective environmental management measures and strategies such as maintaining forest vegetation and wetlands to mitigate the negative effects must be designed to fit local watershed conditions.