Coastal environments are prone to nutrient contamination as a result of excessive use of fertilizers in paddy agriculture on the land. To detect nutrient increases in coastal areas, researchers have used hyperspectral reflectance response to examine some coastal plants, which have proved to be effective as bioindicators. In this study, field hyperspectral technique was evaluated as a tool to detect nutrient concentrations in two coastal plants, i.e., seagrass (Enhalus acoroides) and brown algae (Sargassum sp.), taken from Banten Bay Indonesia, at laboratory scale. Although our initial experiments are still too few in elucidating an accurate relationship of nutrients and spectral signature, we are pleased to communicate that there is scientific evidence that hyperspectral measurement can be used to detect nutrient concentrations in coastal vegetation. Two types of fertilizers—urea, which contains 46% nitrogen, and triple super phosphate (TSP), which contains 14–20% soluble P2O5, commonly used by the local paddy farmers—were applied to both coastal plants in the aquarium experiment. The results of factorial analysis of variance (ANOVA) tests and pigmentrelated indices have proved that some significant differences exist in several wavelengths in response to the fertilizer treatments. This study revealed that brown algae were more sensitive to the same amount of fertilizer applied than seagrass.