Against the background of global warming, the carbon emission of cities accounts for more than 70%, and its carbon sink increase and emission reduction have become the research focus. The water bodies and green spaces in the urban blue–green space have a synergistic carbon sequestration effect, but current research pays less attention to the small and medium scales. Therefore, taking the waterfront green space on both sides of Qinhuai New River in Nanjing as the research object, this paper explores the impact of the synergy between water and greenery on the carbon sequestration efficiency of green space. The study first estimates the carbon sequestration efficiency of green spaces by integrating measured Leaf Area Index (LAI) data with the mean carbon sequestration rate per unit leaf area for typical tree and shrub species. It then constructs a set of water–green spatial relationship indicators and applies a random forest regression model to identify the key factors influencing carbon sequestration efficiency. Finally, multiple scenario models are developed to simulate the effects of green spaces on CO2 reduction, thereby validating the roles of the identified influencing factors. The study found that waterfront green spaces tended to exhibit slightly higher carbon sequestration efficiency compared with non-waterfront green spaces. The proportion of 10 m forest land area and the proportion of 10–20 m forest land area had a higher impact on the carbon sequestration capacity of waterfront green space; that is, the closer the distance between the green space and the water, the better the carbon sequestration capacity. In order to improve the carbon sequestration efficiency of the waterfront area, the green space should be arranged along the water bank as much as possible, the depth of the green space should be increased, the proportion of the forest land area should be increased, the arbor and shrub should be planted evenly, and ribbon planting should be avoided. The study confirmed the synergistic effect of water and greenery in carbon sequestration benefits, providing data support and theoretical reference for the optimization and renewal of urban waterfront green space, and contributing to the realization of urban waterfront green space planning, design, and renewal with the goal of a high carbon sink.