Barnegat Bay has been experiencing a decline of Zostera marina, the important ecosystem engineer which provides a diverse suite of services which increase the diversity and productivity of coastal ecosystems. As efforts are made to reduce those stressors negatively impacting submerged aquatic vegetation health, primarily euthrophication, monitoring is necessary to assess the efficacy of these measures and the role of water quality on overall habitat resiliency. The objective of this project was to provide ongoing quantitative measures on the health of the primary indicators, submerged aquatic vegetation, at a subset of sites throughout northern, central and southern Barnegat Bay. The northern region was dominated by Ruppia maritima and the southern region by Zostera marina, with a transitional zone in the central region. Aboveground biomass of Zostera marina indicates there may be a recovering population within the Bay; however, this may be attributed to annual and seasonal variations rather than an upward trend. Continued monitoring is necessary to elucidate any trends. In those central regions with increasing cover by Ruppia maritima, future work is necessary to determine if Ruppia maritima can provide equivalent habitat and ecosystem services as Zostera marina. The majority of macroalgae sampled was in the form of clumped drift algae, which has a temporary impact on Zostera marina and Ruppia maritima health when compared to longer residence blooms. Linkages between these basal primary producers and upper trophic levels is well documented and the future state of Barnegat Bay fauna, including recreationally and commercially important fish and invertebrate species, will be determined by the resilience of this vegetation in the face of changing water quality parameters.