The detection of invasive plant species in aquatic ecosystems is important to help in the control or to mitigate its spread and impacts. Remote sensing (RS) can be explored in this context, helping to monitor this type of plants. This study intends to present a free to use and open-source software application that, through a graphical user interface, can process remote sensed data to monitor the spread of invasive plant species in aquatic environments, enabling a multi-temporal monitoring. Both unmanned aerial vehicle and satellite-based data were used to validate the potential of the proposed application. A site containing water hyacinth (Eichhornia crassipes) was selected as case study. Both RS platforms provided effective data to detect the areas containing water hyacinth. Thus, this tool provides an alternative and user-friendly way to include RS-based data in ecological studies allowing the detection of invasive plants in water channels.