The present study was undertaken in order to analyse whether macrobenthic communities can or not be used in monitoring programmes of the environmental quality of fish ponds. Functional community analysis and biotic metrics were analysed aiming at the assessment of their effectiveness in discriminating potential impacts of fish production in these systems. The macrofaunal patterns in earthen fish ponds of the Ria Formosa lagoon showed to be influenced by the input of fish food during the production cycle and by changes in abiotic parameters caused by seasonality and fish production. Polychaetes were generally dominant considering the number of taxa and abundance. The trophic functional analysis of the benthic communities showed that the deposit-feeding functional group dominated in both areas of the ponds but within water entrance areas there was an increase of suspension-feeding, carnivory and herbivory feeding modes. The presence of less trophically mixed communities within feeding areas may be related to the relative high disturbance levels of these areas. From the biotic indicators that show a differential response to organic input in fish earthen ponds, the abundance of Capitella spp. as well as the diversity (Shannon–Wiener and Margalef species richness), evenness (Pielou) and AMBI indices seem to be the best indicators to be used in monitoring studies in similar systems. Managers should pay particular attention when Capitella spp. taxa are observed within the feeding areas. Nevertheless, manipulative experiments are needed in order to test the dominance levels of Capitella spp. and the values of those indices that are of concern.