Benthic, water and sediment samples were collected at Okobaba, a sawmill site, and Iddo, a sewage dumpage site, in an open estuarine lagoon, in southwestern Nigeria during two periods (December 1999-May 2000 and April 2002-September 2002). Air, surface and bottom water temperatures were high (23.9-32.0 degrees C). Dissolved oxygen (DO) was between 3.4-5.3 mg/l, while biochemical oxygen demand (BOD) varied between 18.0 and 30.0 mg/l at Iddo and, 7.5 and 8.6 mg/l at Okobaba. The pH was alkaline throughout the sampling period at the two sites (7.3-8.6) while, rainfall was between 0.00 and 372.1 mm. Sediment ranged from mud, sandy mud, muddy sand to sandy type. Density and diversity of macrobenthic fauna were low and representative of Polychaeta, Mollusca and Arthropoda. Factors affecting the dynamics and reduction of species in the two communities were discussed.