The effects of solid organic wastes from a marine fish farm on sediments were tested using benthic community as ecological indicators and biomarkers in native clam (. Scrobicularia plana) as biochemical indicators. The benthic fauna and clam samples were collected in the intertidal sediment in October 2010 from five sites of the Rio San Pedro (RSP) creek, following a gradient of contamination from the aquaculture effluent to the control site. Numbers of species, abundance, richness and Shannon diversity were the biodiversity indicators measured in benthic fauna. Morphological and reproduction status of clams were assessed using the condition factor and gonado-somatic index, respectively. Phase I and Phase II detoxification enzymatic activities (ethoxyresorufin O-deethylase (EROD), glutathione S-transferase (GST)), antioxidant enzymatic activities (glutathione peroxidase (GPX), glutathione reductase (GR)) and oxidative stress parameters (Lipid Peroxidation (LPO) and DNA strand breaks) were measured in clams' digestive gland tissues. In parallel, temperature and salinity in the adjacent water, redox potential, pH and organic matter in sediment, and dissolved oxygen in the interstitial water were measured. The results suggested that RSP showed a spatial gradient characterised by hypoxia/anoxia, reduced potential, acidic conditions and high organic enrichment in sediments at the most contaminated sites. Significant (. p<. 0.05) decrease of biodiversity indicators were observed in the areas impacted by the aquaculture discharges. Biomarkers did not show a clear pattern and of all biochemical responses tested, GPX, DNA damage and LPO were the most sensitive ones and showed significant (. p<. 0.05) increase in the polluted sites. Benthic biodiversity indicators were significantly (. p<. 0.05) positively correlated with pH, redox potential and dissolved oxygen and negatively correlated with organic matter. On the contrary, antioxidant enzymatic responses (GPX) and oxidative stress parameters were significantly (. p<. 0.05) negatively correlated with those physico-chemical parameters. It has been demonstrated that effluents from fish aquaculture activities in Río San Pedro creek may produce an alteration of physico-chemical characteristics of seabed and induce oxidative stress and DNA damage in soft-sediment species which may lead to changes of the benthic population structure and health status of the exposed organisms.