It has been assumed that because seagrasses dominate macrophyte biomass in many estuaries they also dominate primary production. We tested this assumption by developing three carbon budgets to examine the contribution of autotrophic components to the total ecosystem net primary production (TENPP) of Lower Laguna Madre, Texas. The first budget coupled average photosynthetic parameters with average daily irradiance to calculate daily production. The second budget used average photosynthetic parameters and hourly in situ irradiance to estimate productivity. The third budget integrated temperature-adjusted photosynthetic parameters (using Q₁₀=2) and hourly in situ irradiance to estimate productivity. For each budget TENPP was calculated by integrating production from each autotroph based on the producers’ areal distribution within the entire Lower Laguna Madre. All budgets indicated that macroalgae account for 33–42% of TENPP and seagrasses consistently accounted for about 33–38%. The contribution by phytoplankton was consistently about 15–20%, and the contribution from the benthic microalgae varied between 8% and 36% of TENPP, although this may have been underestimated due to our exclusion of the within bed microphytobenthos component. The water column over the seagrass beds was net heterotrophic and consequently was a carbon sink consuming between 5% and 22% of TENPP, TENPP ranged between 5.41×10¹⁰ and 2.53×10¹¹ g C yr⁻¹, depending on which budget was used. The simplest, most idealized budget predicted the highest TENPP, while the more realistic budgets predicted lower values. Annual production rates estimated using the third budget forHalodule urightii andThalassia testudinum compare well with field data. Macroalgae and microalgae contribute 50–60% of TENPP, and seagrass may be more important as three-dimensional habitat (i.e., structure) than as a source of organic carbon to the water column in Lower Laguna Madre.