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Floodplain ecosystems that are characterized by high habitat heterogeneity and hydrological connectivity are considered hotspots for freshwater biodiversity. However, these biodiversity-rich areas have been seriously threatened by biological invasions. The signal crayfish (Pacifastacus leniusculus) is listed as 100 of the world's worst invasive species, and is a major threat to freshwater biodiversity and ecosystem functioning. Here, we examined environmental factors relating to the invasion success of signal crayfish and their morphological responses in floodplain waterbodies. Classification and regression tree analyses showed that most of the influential factors differed between tributary and lake populations. In floodplain tributaries, the occurrence of crayfish was positively related with water temperature and abundance of leaf cover, while crayfish abundance was highest where large-wood was abundant. In floodplain lakes, crayfish were absent at oxygen-poor sites, and abundant at sites with high connectivity to a main channel. These results indicate that conservation practitioners should consider different environmental factors in accordance with strategies for invasive species management (i.e., offensive or defensive management). Furthermore, we demonstrated morphological differences between tributary and lake populations, with tributary crayfish having wider chelae. These morphological differences might have resulted from the physical differences between the two types of waterbodies, facilitating the rapid invasion of signal crayfish to floodplain waterbodies. Our study showed that invasion-risk assessments should consider both environmental factors and morphological responses to new environments to understand invasion ecology and to form effective conservation plans and to prioritize management actions.