Texas A&M University-Corpus Christi (TAMUCC) will improve water quality monitoring methodology of seagrass-dominated ecosystems by developing a database to archive data and images, facilitate analysis and disseminate results. Seagrass blades, collected in the field, will be scanned with the hyperspectral imaging system in the field to collect spatial (picture-like) information and spectral response of the blades and its colonies, then returned to the lab and scanned on high quality color and fluorescence scanners. Images will be analyzed using appropriate software for percent epiphyte cover, epiphyte assemblage structure to the lowest practical taxon, and spatial gradients in epiphyte cover on the seagrass blade. Imaging analyses will be calibrated by epiphyte pigment analyses and traditional measures. Diagnostic pigment biomarkers are a rapid means for assessing algal community composition. The final product will be a set of imaging and analytical routines that can be readily and efficiently adopted for large numbers of samples using relatively simple technology, a prototype database and education/outreach materials.