In the present study, we used the axis model in the spatial syntax approach to analyze the evolution of the water system in Suzhou, China, from the 13th to the 20th centuries and its relationship with the distribution of gardens in the city. The distribution of the authoritative mainstream gardens appeared to be directly affected by the water system, and the gardens located in the areas with high water integration in each period were well preserved. From the 13th to the 17th centuries, gardens in areas with high water integration were all owned by the government and the class with social authority. This was consistent with the patterns for the hierarchical distribution of traditional urban space in China. However, in the 19th century, the gardens in areas with high water integration were owned by the class with social authority and the merchant class, reflecting characteristics different from the traditional pattern. The temple gardens in commercial areas with high water system integration were well preserved. Given the disruption of the surrounding water system, their original isolation from the water system was averted, turning them into public areas for social and public activities. In the 13th and 17th centuries, gardens located in areas with high and low water system integration took advantage of the surrounding water systems for landscaping, demonstrating the gardening principle according to local conditions. However, in the 19th and 20th centuries, the water system decreased sharply in many areas, and gardens built in areas with high water system integration were no longer thus situated. Traditional techniques for diverting water into gardens gradually disappeared. This study revealed that the preservation of gardens in Suzhou was largely due to the pattern of their distribution in the urban structure, and the gardens preserved to date have benefited from their location relative to the urban spatial structure of the 19th century. Private gardens, which embody the elegant taste of the literati, strongly resisted the aesthetic invasion from commercialization, however, and were also developed and preserved. Their social and spatial attributes were transformed by commercialization, presenting a contradictory yet complementary relationship between traditional garden culture and commercial development in Suzhou.