Oyster reefs are a primary source of calcium carbonate in most estuaries and the habitat complexity provided by these reefs supports a diversity of estuarine life. The available surface area of hard substrate on an oyster reef is critical for population maintenance, as this substrate provides habitat for the settlement of new oyster recruits. On natural reefs, the primary substrates available for settlement by spat include live oysters, boxes (dead articulated valves), and cultch (single oyster shells and shell fragments). Data from a long-term oyster monitoring program from February 2016 to October 2020 were used to generate a monthly time series of the percent of total carbonate weight contributed by live oysters, boxes, and cultch at four reefs in the Mississippi Sound. These percentages vary spatially and temporally. When reefs were healthy, live oysters dominated the total carbonate. During the study period, two mass mortality events occurred. Following the 2016 mortality event, the substrate contributing the majority of the carbonate shifted from live oysters to cultch at all reefs sampled. Three reefs exhibited a modest population recovery following the mortality event only to be impacted by a second, more severe mass mortality event in 2019. Boxes usually had the highest number of spat per gram carbonate at all reefs. The potential surface area (PSA) of each substrate type was calculated by comparing the available surface area of each substrate type and the number of spat that settled on each substrate. Correction factors were generated to account for larval settlement preferences and used to either debit or credit the PSA to calculate effective surface areas (ESA) for each substrate type. Cultch offered the highest ESA at Pass Christian, and cultch ESA was higher than box ESA at Henderson Point and Between Bridges reefs. At Bay St. Louis, box ESA was twice that of cultch. These results suggest cultch and boxes are more valuable settlement substrates than live oysters in this region under the conditions present during the survey time frame, which was characterized by low oyster abundance and aperiodic mass mortality. The unbalanced ESA, in which live oyster ESA is underrepresented, represents an unhealthy condition and demonstrates that a critical period exists for reef recovery after mass mortality in which the timely coincidence of increased box ESA and larval availability is essential for rapid recovery from mass mortality.