We tested a supervised classification approach with Landsat 5 Thematic Mapper (TM) data for time-series mapping of seagrass in a subtropical lagoon. Seagrass meadows are an integral link between marine and inland ecosystems and are at risk from upstream processes such as runoff and erosion. Despite the prevalence of image-specific approaches, the classification accuracies we achieved show that pixel-based spectral classes may be generalized and applied to a time series of images that were not included in the classifier training. We employed in-situ data on seagrass abundance from 2007 to 2011 to train and validate a classification model. We created depth-invariant bands from TM bands 1, 2, and 3 to correct for variations in water column depth prior to building the classification model. In-situ data showed mean total seagrass cover remained relatively stable over the study area and period, with seagrass cover generally denser in the west than the east. Our approach achieved mapping accuracies (67% and 76% for two validation years) comparable with those attained using spectral libraries, but was simpler to implement. We produced a series of annual maps illustrating inter-annual variability in seagrass occurrence. Accuracies may be improved in future work by better addressing the spatial mismatch between pixel size of remotely sensed data and footprint of field data and by employing atmospheric correction techniques that normalize reflectances across images.