Aquaculture effluents are rich in nitrogen compounds that may enhance local primary productivity, leading to the development of algae blooms. The goal of this study was to assess the potential use of naturally occurring green macroalgae (Ulva and Enteromorpha) as bioremediators for nitrogen-rich effluents from a fish aquaculture plant, by evaluating their respective uptake dynamics under controlled conditions. Ulva and Enteromorpha were incubated separately in aquaculture effluent from a local pilot station. Algae tissue and water samples were collected periodically along 4 h. For each sample, nitrate, nitrite, and ammonia concentrations were quantified in the effluent, while internal algae reserve pools and nitrate reductase activity (NRA) were determined within the algae tissues. Both macroalgae absorbed all dissolved inorganic nitrogen compounds in less than 1 h, favoring ammonia over nitrate. Ulva stored nitrate temporarily as an internal reserve and only used it after ammonia availability decreased, whereas Enteromorpha stored and metabolized ammonia and nitrate simultaneously. These distinct dynamics of ammonia and nitrate uptake supported an increase in NRA during the experiment. This study supports the hypothesis that Ulva or Enteromorpha can be used as bioremediators in aquaculture effluents to mitigate excess of dissolved inorganic nitrogen.