Estimating the economic value of ecosystem services derived from estuarine habitats is important for prioritising management, conservation, and restoration activities, but remains challenging. Recently, a novel approach to estimate the value of estuarine habitats for species commercially harvested from estuaries was developed, which incorporates Bayesian stable isotope mixing models that identify the underlying primary production responsible for the nutrition of these species and links this to the value of product for fisheries. However, the difficultly of separating common primary nutrient sources in estuaries; saltmarsh grass (Sporobolus virginicus) and seagrasses, means application of this approach has been constrained to estuaries with little or no seagrass. Here, we extend this approach and examine the use of tri-variate (C, N and S) isotopic composition to model the comparative economic value of saltmarsh, seagrass, and other producer groups, for a commercial fishery. Isotope data indicated that grouped estuary producers contributed 44 ± 16% (mangrove and saltmarsh succulents), 22 ± 11% (saltmarsh grass), 11 ± 6% (fine benthic organic matter) and 23 ± 11% (seagrasses) of exploited species diets. Although seagrass and saltmarsh contributions were reasonably similar, the areal coverage of saltmarsh habitats was ∼10% that of seagrasses. This affected the area-standardised valuation of these habitats, which suggested that saltmarsh had the highest value (AUD $621 ± 191 ha−1y−1) followed by mangroves (AUD $227 ± 66 ha−1y−1), while seagrasses had the lowest value (AUD $63 ± 29 ha−1y−1). These results highlight the impact of areal coverage on the comparative value of estuarine habitats, but also highlight that habitats with lesser areal extent but higher proportional contribution to diets of exploited species may present a higher priority for conservation or repair.