Eelgrass in the Great Bay Estuary in 2009 was once again present only in Great Bay itself and in Portsmouth Harbor. For the second year in a row, there was no eelgrass in Little Bay or in the Piscataqua River. In 2009, there was a continued loss of eelgrass biomass in Great Bay; there has been a 66.4% loss of biomass in Great Bay since 1996 and distribution is 30% less than in 1996. Although eelgrass distribution in Great Bay itself increased between 2008 and 2009, primarily due to continued expansion from natural seeding of bare areas, the Bays eelgrass biomass continued to decline as a result of decreases in plant density in existing beds. Nuisance macroalgae in Great Bay continued to proliferate and impact eelgrass by smothering eelgrass shoots and reducing shoot density. In 2009, Portsmouth Harbor experienced a 16% loss of eelgrass distribution since 2008, for a loss of 31% of the Harbors eelgrass distribution in the past three years, an alarming trend. Although the number of acres of eelgrass has increased, driven by gains in Great Bay, even with these areal gains, biomass is down for the Bay itself and the trends of loss in Portsmouth Harbor of both eelgrass distribution and percent cover continue. Despite the increase in eelgrass distribution in Great Bay Estuary due to the increased seed recruitment in Great Bay, the loss of percent cover and biomass in Great Bay and in Portsmouth Harbor again this year (2008-2009) indicate the continuing adverse water quality conditions in the Estuary.