The physical characteristics (temperature, salinity, pH and dissolved oxygen), turbidity, phytoplankton biomass (Chlorophyll-a) and nutrients in the coastal waters of a stressed area of the Nile Delta were studied biweekly from January to December 2007. The results indicated that the discharged waste waters caused pronounced changes in the water quality. The surface salinity recorded a minimum of 0.3 ‰ at site IV and a maximum of 38.1 ‰ at site I. pH ranged from 7.25 at site V to 8.55 at site II, while dissolved oxygen attained the lowest concentration (0.5 mg/l) at sites IV and V, and the highest concentration (10.82 mg/l) at site II. The water turbidity demonstrated wide fluctuation between 0.2 NTU at site II and 117 NTU at site III. The nutrient salts experienced great variation throughout the area of study as well as on the time scale; nitrate showed a range of 3 – 1682 µg/l, nitrite: 0.42-1106.2 µg/l, ammonia displayed undetectable level as well as high concentration (1646.6 µg/l), while the total phosphorus fall within a range of 10-8260 µg/l and silicate of 40 – 40800 µg/l. High phytoplankton biomass was recorded over the whole area (chl. a: 0.4 - 197.4 µg/l). The trophic state of the study area calculated by trophic index (TRIX) appeared to be widely different, reflecting degraded and very high trophic water, except at site I which contained moderate quality and high trophic water in significant part of the year.