In the face of the climate crisis, more and more attention has been paid to the adaptation strategy and resource management of water resources, but the construction of large-scale water infrastructure has also caused many controversies. This study will point out the controversy over Kinmen’s transboundary water diversion and the importance of understanding the dilemma of water resources governance in border islands from the perspective of border governance. By reviewing the formation, predicament and transformation of Kinmen’s water supply network since the military administration period in the 1950s, this paper divides Kinmen’s water supply network into two periods: “reservoir construction” from 1950s to 1990s and “pipeline politics” from 2000 onwards. The former is that the state has led the construction of water conservancy facilities for the sake of border governance, while the latter is that water resources governance has loosened the state’s dominance in border governance. This article will point out that although the transboundary water diversion project started by the Kinmen County government after 2000 was a policy driven by geopolitical changes, the borders did not disappear. On the contrary, borders are ubiquitous in the daily practice of water resources governance constructed by the local government to monitor water quality. The real border practice is not an administrative border under a national agreement, but a heterogeneous network of tiny physical facilities such as numbers, checkpoints, and cisterns, and its political effect is no less than that of dams and canals. and other large water infrastructures.