In the course of its environmental monitoring activities, the Scottish Government’s Marine Directorate collects a large amount of underwater video to, for example, obtain information on the numbers of fish in rivers or on species living on the seabed. Manual analysis of this footage is laborious and costly, but Machine Learning algorithms can now be used to automate such image analysis. The Marine Directorate commissioned the University of East Anglia to develop a web-based application to allow staff to create, train and execute machine learning-based (semi-)automated analysis of video footage without a need to interact with the underlying computer code. The application was tested using three diverse sets of video footage and found to be usable by staff without computer science or coding experience. The tool was able to detect and count sea pens in footage from towed underwater vehicles, salmon smolts at sea in underwater footage from towed fishing gear and adult salmon and sea trout in footage from underwater or overhead cameras at fixed locations on rivers. Improving the accuracy of the models at detecting and counting organisms of interest will require the use of larger annotated datasets in further training of the algorithms, but the current application provides a basis for further developing these.