We studied the effects of a waste water treatment plant on organic matter dynamics in Fosso Bagnatore, a Mediterranean stream near Rome (Italy). Concentrations of dissolved organic carbon and seston, along with the standing crops of coarse benthic organic matter and fine benthic organic matter, were monitored monthly during 2002 in two reaches situated upstream and downstream of a waste water treatment plant effluent. Additionally, we examined two stream functional characteristics: whole stream metabolism, which was measured from diel changes in oxygen concentrations, and nutrient removal, which was studied by experimental additions of NH4-N, NO3-N and PO4-P. The possible influence of WWTP organic matter alterations on ecosystem functioning was addressed by measuring epilithon characteristics (standing crop, C:N:P ratios and chlorophyll a content). The WWTP effluent caused an increase (several-fold) of DOC and seston concentrations, and FBOM standing crop, moreover it modified their temporal variation. Downstream of the wastewater treatment plant we detected an higher heterotrophic microbial biomass and a correspondent higher community respiration. The uptake of NH4-N, NO3-N and PO4-P was highly variable probably as consequence of the high variability of the compartments involved (e.g. DOC, FBOM, community respiration). We showed that WWTP effluent altered the organic matter dynamics of this Mediterranean-type headwater stream and that these effects were reflected in its ecosystem functioning. Because of the linkage of headwaters to downstream ecosystems and due to their significant role in landscape and catchment processes, the alterations of organic matter dynamics that we detected at a local scale may have important consequences on a broader scale.