A detailed submerged aquatic vegetation (SAV) study was conducted in Little Egg Harbor (39°35′N, 74°14′W), New Jersey, a lagoonal estuary located within the boundaries of the Jacques Cousteau National Estuarine Reserve, to assess the demographic characteristics and spatial habitat changes of Zostera marina beds over an annual growing period and to determine the species composition, relative abundance, and potential impacts of benthic macroalgae on seagrass habitat in the system. Two disjunct seagrass beds in Little Egg Harbor, covering an area of ∼1700 ha, were sampled at 10 equally spaced points along six, east–west-trending transects in spring, summer, and fall (June–November) of 2004. During this period, 180 seagrass samples were collected at 60 transect sites, together with an array of water quality measurements. Results of this investigation indicate that both aboveground and belowground biomass of seagrass peaked during June–July and declined significantly into the fall months. Mean aboveground biomass ranged from 18.22 to 106.05 g dry wt m−2, and mean belowground biomass from 50.48 to 107.64 g dry wt m−2. Biomass values were higher along the northernmost sampling transects than along those farther to the south. They were also higher at interior sampling sites within the seagrass beds than along the bed margins for two of the three sampling periods. Mean seagrass blade length was consistent throughout the study period, averaging 31.83–34.02 cm. The percentage of cover by seagrass, which ranged from 21% to 45%, peaked in June–July at the time of maximum seagrass biomass. The percentage of cover by macroalgae was lower than that of seagrass, averaging 13%–21%, with maximum cover occurring in August–September. Most of the macroalgal species collected in the seagrass beds were red algae, although the dominant species was typically the green seaweed, Ulva lactuca. During the 6-month study period, no brown tide (Aureococcus anophagefferens) blooms were recorded, and phytoplankton abundance did not appear to cause shading problems for seagrass in the system. However, benthic macroalgal blooms were observed in the seagrass beds, most notably U. lactuca. These blooms blanketed parts of the seagrass beds and appeared to degrade them over extensive areas. Nutrient enrichment, elevated turbidity levels, and prop scarring are anthropogenic factors that may significantly influence seagrass beds in Little Egg Harbor during the growing season.