Sediment porewater nutrients often occur at concentrations that are orders of magnitude higher than nutrients in overlying waters, and accordingly may subsidise growth of benthic macroalgal mats in estuarine ecosystems. The relative contribution of porewater nutrients is expected to be particularly important for macroalgae entrained in intertidal mudflat sediments, where access to water column nutrients is tidally constrained. In this study, filamentous Gracilaria chilensis thalli were simultaneously exposed to sediment and overlying water nutrient sources, labelled using 15N tracers (15NH4+ or 15NO3−) during a 5-day experiment. Dissolved inorganic N (DIN) uptake from porewater and overlying water accounted for 33 and 52%, respectively, of the N estimated as necessary to support the growth of G. chilensis, despite the two-fold lower DIN concentration of the overlying water and its periodic availability (8 h day−1). Of the total N assimilated by the plants, ~ 15% could not be accounted for, supporting the acquisition of other N forms in order to meet demand. We also found that regardless of background NH4+:NO3− ratios (i.e. 1:3 in overlying water and 12:1 in porewater), plants accumulated 15NH4+ significantly more readily than 15NO3−, indicating a preference for NH4+. This ability to utilise multiple sources and species of N relatively rapidly may partly explain the competitive success of entrained macroalgae relative to non-entrained species and historically abundant seagrass beds in these environments. These results underscore the significance of both internal nutrient loading and external inputs as important in sustaining opportunistic macroalgal blooms in shallow estuaries.