Hydrological processes in lowland polders, especially those for paddy rice planting, are affected by complicated factors. The improved Wageningen Lowland Runoff Simulator (WALRUS) model incorporates an irrigation and drainage scheme, and a new stage–discharge relationship to account for hydrological processes in multi-land-use polder with paddy fields and pumping stations. Here, this model was applied to assess how climate and land use changes affected the runoff of a Chinese polder in Poyang Lake basin in the past two decades. Simulated results showed that the runoff in the autumn–winter transition and midsummer months increased significantly, whereas those in the other months decreased slightly during the period of 1996–2005, primarily affected by climate change. For the period of 2006–2014, the runoff in the autumn–winter transition and midsummer increased, while that in the other months declined, affected by both climate and land use/cover changes. The land use/cover change resulting from the conversion of rice–wheat rotation to dominantly double-rice cropping and the expansion of residential area, increased the runoff during this period by demanding more irrigation water from the outside basin.