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Long‐term environmental sustainability and community acceptance of the shrimp farming industry in Australia requires on‐going development of efficient cost‐effective effluent treatment options. In this study, we aimed to evaluate the effectiveness of a shrimp farm treatment system containing finfish and vertical artificial substrates (VAS). This was achieved by (1) quantifying the individual and collective effects of grey mullet (Mugil cephalus L.) and VASs on water and sediment quality, and (2) comparing the retention of N in treatment systems with and without the presence of finfish (M. cephalus and the siganid Siganus nebulosus (Quoy & Gaimard)), where light was selectively removed. Artificial substrates were found to significantly improve the settlement of particulate material, regardless of the presence of finfish. Mullet actively resuspended settled solids and reduced the production of nitrate when artificial substrates were absent. However, appreciable nitrification was observed when mullet were present together with artificial substrates. The total quantity of N retained by the mullet was found to be 1.8– 2.4% of the incoming pond effluent N. It was estimated that only 21% of the pond effluent N was available for mullet consumption. When S. nebulosus was added, total finfish N retention increased from 1.8% to 3.9%, N retention by mullet also improved (78±16 to 132±21‐mg N day−1 before and after siganid addition respectively). Presence of filamentous macroalgae (Enteromorpha spp.) was found to improve the removal of N from pond effluent relative to treatments where light was excluded. Denitrification was also a significant sink for N (up to 24% N removed). Despite the absence of algal productivity and greater availability of nitrate, denitrification was not higher in treatments where light was excluded. Mullet were found to have no effect on the rates of denitrification but significantly reduced macroalgal growth on the surface of the water. When mullet were absent, excessive macroalgal growth led to reduced dissolved oxygen concentrations and nitrification. This study concludes that the culture of mullet alone in shrimp farm effluent treatment systems does not result in significant retention of N but can contribute to the control of macroalgal biomass. To improve N retention and removal, further work should focus on polyculturing a range of species and also on improving denitrification.