Multiple indicators of water quality, sediment quality, and biological condition were used to assess the status of ecological condition of National Estuarine Research Reserve System (NERRS) sites in North Carolina, South Carolina, and Georgia relative to a suite of corresponding scoring criteria. All measurements were made in subtidal aquatic habitats. Calculated scores were integrated into an overall index of habitat quality and used to make comparisons among the various NERR and nonNERR estuaries throughout the region. Sediment quality scores varied considerably among NERR sites, but in most cases were similar between individual NERR and non‐NERR sites in corresponding states. Water quality and biological condition indicators scored consistently higher for NERRs versus non‐NERR sites. Overall habitat quality scores also were consistently higher for NERRS sites, suggesting that these areas are on par with if not in slightly better condition ecologically than neighboring nonNERR estuaries. Portions of individual NERR sites rated as poor with respect to overall habitat quality were limited to relatively small areas (<13% of a reserve’s total sampling area). Integr Environ Assess Manag 2015;11:266–275. Published 2014 SETAC. This article is a US Government work and, as such, is in the public domain in the USA.