Secondary crops provide a means of assimilating some effluent nitrogen from eutrophic shrimp farm settlement ponds. However, a more important role may be their stimulation of beneficial bacterial nitrogen removal processes. In this study, bacterial biomass, growth and nitrogen removal capacity were quantified in shrimp farm effluent treatment systems containing vertical artificial substrates and either the banana shrimp Penaeus merguiensis (de Man) or the grey mullet, Mugil cephalus L. Banana shrimp were found to actively graze biofilm on the artificial substrates and significantly reduced bacterial biomass relative to a control (24.5±5.6 mg C m−2 and 39.2±8.7 mg C m−2, respectively). Bacterial volumetric growth rates, however, were significantly increased in the presence of the shrimp relative to the control (45.2±11.3 mg C m−2 per day and 22.0±4.3 mg C m−2 per day, respectively). Specific growth rate, or growth rate per cell, of bacteria was therefore appreciably stimulated by the banana shrimp. Nitrate assimilation was found to be significantly higher on grazed substrate biofilm relative to the control (223±54 mg N m−2 per day and 126±36 mg N m−2 per day, respectively), suggesting that increased bacterial growth rate does relate to enhanced nitrogen uptake. Regulated banana shrimp feeding activity therefore can increase the rate of new bacterial biomass production and also the capacity for bacterial effluent nitrogen assimilation. Mullet had a negligible influence on the biofilm associated with the artificial substrate but reduced sediment bacterial biomass (224±92 mg C m−2) relative to undisturbed sediment (650±254 mg C m−2). Net, or volumetric bacterial growth in the sediment was similar in treatments with and without mullet, suggesting that the growth rate per cell of bacteria in grazed sediments was enhanced. Similar rates of dissolved nitrogen mineralisation were found in sediments with and without mullet but nitrification was reduced. Presence of mullet increased water column suspended solids concentrations, water column bacterial growth and dissolved nutrient uptake. This study has shown that secondary crops, particularly banana shrimp, can play a stimulatory role in the bacterial processing of effluent nitrogen in eutrophic shrimp effluent treatment systems.