Seawalls are often built along naturally dynamic coastlines, including the upland edge of salt marshes, in order to prevent erosion or to extend properties seaward. The impacts of seawalls on fringing salt marshes were studied at five pairs of walled and natural marshes in the Great Bay Estuary of New Hampshire, USA. Marsh plant species and communities showed no difference in front of walls when compared with similar elevations at paired controls. However, seawalls eliminated the vegetative transition zone at the upper border. Not only did the plant community of the transition zone have high plant diversity relative to the low marsh, but it varied greatly from site to site in the estuary. The effects of seawall presence on other marsh processes, including sediment movement, wrack accumulation, groundwater flow, and vegetation distribution and growth, were examined. Although no statistically significant effects of seawalls were found, variation in the indicators of these processes were largely controlled by wave exposure, site-specific geomorphology and land use, and distance of the sampling station from the upland. Trends indicated there was more sediment movement close to seawalls at high energy sites and less fine grain sediment near seawalls. Both trends are consistent with an increase in energy from wave reflection. The distribution of seawalls bordering salt marshes was mapped for Great and Little Bays and their rivers. Throughout the study area, 3.54% of the marshes were bounded by shoreline armoring (5876 m of seawalls along 165.8 km of marsh shoreline). Localized areas with high population densities had up to 43% of marshes bounded by seawalls. Coastal managers should consider limiting seawall construction to preserve plant diversity at the upper borders of salt marshes and prevent marsh habitat loss due to transgression associated with sea level rise.