An overgrowth of invasive floating macrophytes can occur in shallow eutrophic lakes as a result of significant anthropogenic pressures. This necessitates appropriate monitoring, followed by informed management, control and mitigation actions. In this study, we explored the long-term dynamics of macrophyte stands in a fluvial-wetland system and the influence of mechanical removal alongside environmental drivers. The Landsat imagery archive was used to analyze the areal coverage and canopy density of both autochthonous and allochthonous macrophytes in the Mantua lakes system (Northern Italy). Satellite derived data showed a substantial increase in the extent of the alien Nelumbo nucifera, and Ludwigia hexapetala, and the native Trapa natans over a timescale of decades, possibly caused by the temporary absence of macrophyte removal and altered hydrology. According to spectral proxies, N. nucifera recorded consistently the highest density in the system. T. natans density was found to respond to the maximum summer temperature and Eastern Atlantic climatic index, reflecting the role of regional climatic controls. This approach may be transferred to inland waters from regional to global scale exploiting satellite archives to obtain a time series on changing species dynamics essential for the conservation and management of aquatic habitats.