This report documents the results of a comprehensive three-year investigation of the seagrass beds in the Barnegat Bay-Little Egg Harbor Estuary by Dr. Mike Kennish, Scott Haag, and Greg Sakowicz. It reveals significant temporal and spatial variation in seagrass density (shoots m-2), biomass, blade length, and percent cover of bay bottom. Quadrat, core, and water quality sampling at multiple transect sites in four disjunct seagrass beds of the estuary during the June-November period in 2004, 2005, and 2006 yielded more than 1000 abiotic and biotic measurements each year for assessment of seagrass dynamics in the system. The occurrence of brown tide and benthic macroalgal blooms and their potential impacts on seagrass beds in the estuary were also examined.