This user's manual describes the Middle Mississippi River Decision Support System (MMRDSS) and gives detailed examples on its use. The MMRDSS provides a framework to assist decision makers regarding natural resource issues in the Middle Mississippi River floodplain. The MMRDSS is designed to provide users with a spatially explicit tool for tasks, such as inventorying existing knowledge, developing models to investigate the potential effects of management decisions, generating hypotheses to advance scientific under- standing, and developing scientifically defensible studies and monitoring. The MMRDSS also includes advanced tools to assist users in evaluating differences in complexity, connec- tivity, and structure of aquatic habitats among river reaches. The Environmental Systems Research Institute ArcView 3.x platform was used to create and package the data and tools of the MMRDSS.