An ODYSSEY autonomous underwater vehicle (AUV) was deployed in Massachusetts and Cape Cod Bays in September 1998 to collect chlorophyll fluorescence, optical backscattering (880nm), and physical data. It sampled the region mainly in a sawtooth pattern with horizontal resolution between ∼120m at the middle of the water column and with vertical resolution of 0.1m. The data were used to quantify various features in both physical and bio-optical properties in the Bays. In particular, an upwelling front with enhanced chlorophyll fluorescence was found off the coast of Race Point. Chlorophyll patches with along-track spatial scales less than 3.6km were found southeast of Plymouth and southwest of Race Point. Southeast of Plymouth, strong sediment re-suspension was also evident. In the early fall, the water column was characterized by three layers: warm and fresh surface water; cold and salty bottom water; and a transition (pycnocline) layer with sharp vertical temperature and salinity gradients. A relatively thin chlorophyll maximum layer was evident in the strong pycnocline. This work represents one of the first successful applications of AUVs for interdisciplinary coastal research. Our results demonstrate that AUVs can provide high-quality, concurrent measurements of physical and bio-optical properties in a very effective manner. Some future uses of AUVs are suggested.