Eelgrass cover extent is among the most reliable indicators for measuring changes in coastal ecosystems. Eelgrass has colonized the mouth of the Romaine River and has become a part of environmental monitoring there since 2013. The presence of eelgrass in this area is an essential factor for the early detection of changes in the Romaine coastal ecosystem. This will act as a trigger for an appropriate environmental response to preserve ecosystem health. In this paper, a cost- and time-efficient workflow for such spatial monitoring is proposed using a pixel-oriented k-NN algorithm. It can then be applied to multiple modellers to efficiently map the eelgrass cover. Training data were collected to define key variables for segmentation and k-NN classification, providing greater edge detection for the presence of eelgrass. The study highlights that remote sensing and training data must be acquired under similar conditions, replicating methodologies for collecting data on the ground. Similar approaches must be used for the zonal statistic requirements of the monitoring area. This will allow a more accurate and reliable assessment of eelgrass beds over time. An overall accuracy of over 90% was achieved for eelgrass detection for each year of monitoring.