Trophic composition of free living nematodes within different stations at Rosetta estuary (RE) and Eastern Harbor of Alexandria (EH) was examined. Sediments at the highly dynamic RE were subjected to intense wave action and supported significantly (P<0.05) lower mean nematode density (<5 individuals per 10cm") than sediments within the EH. Mean nematode densities and numerical trophic abundance were highest at the semi- closed basin (p<0.05) that sheltered from liydrodynamic induced disturbance. The higher nematode abundance at EH was due to availability of food sources and heterogeneous sediment, whereas the lower nematode abundance at RE was due to homogenous sand and highly dynamical process. According to Jensen's classification (1987) trophic levels were composed of four guilds at both locations (deposit feeders, epistrate feeders, scavengers and predators). Deposit feeders dominated at the two locations (46.5% and 37% respectively at RE and EH) probably due to prevalence of fine and very fine sands and the high load of organic matter. Sediment characteristics and high load of organic matter appeared to be the limiting factors controlling the relative importance of nematode trophic guilds at RE and EH. The Univariate (ANOVA) and multivariate (PERMANOVA) analyses indicated that total nematode abundance and its trophic guilds were distinct between locations and among dates. No significant variation among or within stations except for scavengers. The extent to which the macro-sc.:le (Km) variability was more important than micro-scale (m) variability was tested and revealed the higher variability on larger scale than on smaller scale due to physical, hydrodynamic process as well as sediments characteristics.