This work describes the water collection experiment component of the Megacollect 2004 campaign. Megacollect was a collaborative campaign coordinated by RIT with several institutions to spectrally measure various target/background scenarios with airborne sensors and ground instruments. An extension to the terrestrial campaign was an effort to simultaneously measure water optical properties in different bodies of water in the Rochester Embayment.This collection updates a previous effort in which water surface measurements were made during an AVIRIS mission over the Rochester Embayment (May 1999). Megacollect 2004 builds on this through an expanded campaign that increased the number of stations sampled, extended the spectral range of measurements, and improved the spatial resolution of the imagery through the use of multiple sensors (COMPASS, SEBASS, MISI, WASP). A larger set of in-water instruments were deployed on several vessels to sample and measure water optical properties near the shores of Lake Ontario, the northern portions of Irondequoit Bay, and several smaller ponds and bays in the Rochester Embayment. This paper describes the different in-water instruments deployed, the measurements obtained and how they will be used for future modeling efforts and development of hyperspectral algorithms.