We studied the effects of a waste water treatment plant on organic matter dynamics in Fosso Bagnatore, a Mediterraneanstream near Rome (Italy). Concentrations of dissolved organic carbon and seston, along with the standing crops of coarse benthicorganic matter and fine benthic organic matter, were monitored monthly during 2002 in two reaches situated upstream anddownstream of a waste water treatment plant effluent. Additionally, we examined two stream functional characteristics: wholestream metabolism, which was measured from diel changes in oxygen concentrations, and nutrient removal, which was studiedby experimental additions of NH4-N, NO3-N and PO4-P. The possible influence of WWTP organic matter alterations on ecosystemfunctioning 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, moreoverit modified their temporal variation. Downstream of the wastewater treatment plant we detected an higher heterotrophic microbialbiomass and a correspondent higher community respiration. The uptake of NH4-N, NO3-N and PO4-P was highly variableprobably as consequence of the high variability of the compartments involved (e.g. DOC, FBOM, community respiration). Weshowed that WWTP effluent altered the organic matter dynamics of this Mediterranean-type headwater stream and that theseeffects were reflected in its ecosystem functioning. Because of the linkage of headwaters to downstream ecosystems and due totheir significant role in landscape and catchment processes, the alterations of organic matter dynamics that we detected at a localscale may have important consequences on a broader scale.