We examined the effects of the discharge from a wastewater treatment plant (WWTP) on the interstitial water chemistry and structure of the hyporheos in two sections of the La Tordera stream, one upstream and one downstream of the effluent from the treatment plant. Interstitial water samples were collected to determine the vertical hydraulic gradient (VHG) and hydraulic conductivity (K) at six sites in each of the two sections on six occasions between November 2006 and September 2007. Samples of the interstitial meiofauna were collected in upwelling zones in both sections of the river. There were no patterns in the hydraulic gradient either in its direction or its magnitude along the longitudinal axis. There were no differences in VHG recorded at the sites sampled indicating that the two sections were similar in terms of geomorphology. The hydraulic conductivity was greatest in the control section (upstream of the effluent) of the stream. There were no significant differences in specific conductance, phosphates, nitrates or ammonia in the upwelling and downwelling zones. In the upwelling zones in the section of the river downstream from the effluent the concentrations of nitrates were greater than in the downwelling zones, but levels of phosphates and ammonia were lower. There was a decrease in the interstitial nutrient concentrations along a longitudinal gradient downstream of the effluent. A total of 24 taxa were collected from the hyporheos, with Chironomids and Oligochaetes being the most abundant groups. A higher Shannon diversity index (2.86) was recorded in the downstream section of the river even though a greater taxa richness (18) was recorded in the control section. This is probably due to the fact that a larger number of rare or unusual species was found in this section. According to the BMWP biological index the water quality in the control and downstream sections was polluted and heavily polluted, respectively. The shifts in hydraulic exchange processes and the bio-physicochemical environment of the hyporheic zone are the main effects of the discharge from the Santa Maria Palautordera wastewater treatment plant on the two sections of the river studied.