The physical and chemical changes in sediment and near bottom water caused by clam dredging were examined during July and September 1999, at two locations Vilamoura (VL) and Armona (AR), south coast of Portugal. Sediment cores and near bottom water were collected simultaneously before dredging (control samples) and within short time intervals (min-h) after dredging. After dredging operations, microphytobenthos coming from the path were accumulated in the re-worked sediment (ridge). Chlorophyll a in superficial sediment increased from 1.2 microg x g(-1) before dredging to 1.7 microg x g(-1) after dredging and these higher values remained for a few hours. However, the expected increase of chlorophyll a in near bottom water due to re-suspension was not observed. After sediment disturbance an instantaneous sorption of phosphorus onto iron oxides occurred in the upper sediment layers (from 2 to 3 micromol x g(-1) before dredging to 4-5 micromol x g(-1) after dredging). A microcosm experiment showed that after sediment disturbance HPO(4)(2-) dissolved in pore water decreased from 40 to 10 microM being simultaneously sorbed onto iron oxides formed in the top layer of sediment. The ammonium, nitrates, organic nitrogen, phosphate and silicate dissolved in pore water decreased immediately after dredging activity and simultaneously an increase in near bottom water was sporadically observed. Generally, the re-establishment of seabed was reached within a short time (min-h), at both stations (VL and AR).