Alien species invading freshwater systems are causing major changes in biodiversity worldwide. Some alien species have been used as indicators of water quality and environmental degradation. We discuss the reasons for monitoring invasive species beyond their use as ecological indicators, and offer guidance on the design of appropriate long-term monitoring schemes. Monitoring plays an essential role in providing an early warning system, because eradication of alien species at the early stages of invasion is more effective and less costly than when the invader is established. Monitoring the presence of aliens is also more effective when associated to monitoring the vectors known to transport them, and is equally valuable after eradication and to determine the effects management and whether restoration has been achieved. Scientifically, monitoring an invasion in conjunction with measuring other abiotic and biotic parameters provides baseline information on the dynamics of the invasion, the vulnerability of the habitat to invasion and on the impacts of the invader. Combining information on the patterns of invasion with that of the regional environmental factors operational at the time is relevant to establishing relationships between the invasion and other global change components. Overall, the long-term monitoring of biological invasions, that integrates information before, during and after an invasion provides valuable information for both managers and scientists