Sediment cores were taken from impacted and non-impacted areas and subjected to different incubations: (i) uninoculated, (ii) inoculated with fish feed and (iii) inoculated with gilthead seabream (Sparus aurata) faeces. After inoculation (or not), the cores were incubated for 8 h and the following biogeochemical fluxes were determined: sediment oxygen uptake (SOU), total ammonia nitrogen flux (TANf) and the production of acid volatile sulphides (AVS-Sp). The results showed that the impacted sediments had a more pronounced benthic metabolism than non-impacted sediments. Correlations between the variables and factorial analysis showed that oxygen consumption caused by the organic enrichment appeared as the trigger for subsequent biogeochemical alterations. The addition of faeces led to proportionally higher benthic rates of SOU, TANf and AVS-Sp than those obtained in the feed incubations. Although the feed is relatively sterile and does not create an oxygen demand until colonized by bacteria, the faeces are already richly colonized with fish gut bacteria and could start to consume oxygen without the lag phase experienced in the incubations with feed. The TANf values measured after the addition of feed or faeces seem to be more related to the leaching velocity of TAN than with the benthic flux, given the short incubation time.