Temporal and spatial variation in soft-bottom benthic communities following recovery from a pollution episode were studied between January and September 2004 in and around Alsancak Harbor, located in the polluted part of Izmir Bay (Aegean Sea, eastern Mediterranean). Samples were collected at seven stations by van Veen grab. Three additional stations were sampled by means of a beam trawl to take into account large mobile animals and for a better estimate of the local biodiversity. A total of 231 species belonging to 10 zoobenthic groups were found. Polychaetes contributed 90% of the total faunal populations and mollusks 87% of the total biomass in the area. Community parameters varied significantly among stations and sampling periods; number of species ranged from 2 to 79 per 0.1 m2 grab sample; density from 20 to 81,720 ind·m−2; biomass from 0.1 to 4190 g·m−2; Shannon–Wiener diversity index (log2 base) from 0.4 to 4.4; and Pielou's evenness index from 0.11 to 1.0. Collections indicate that a number of species, including those sensitive to pollution, have colonized the area where azoic conditions had been previously reported. A total of six exotic species, Streblospio gynobranchiata, Polydora cornuta, Hydroides dianthus, Hydroides elegans, Anadara demiri and Fulvia fragilis, probably transferred to the area via ballast water or hull fouling, dominated soft or hard substrata in and near Alsancak Harbor. The first two species accounted for more than 70% of the total population in the area, while A. demiri contributed the most to the biomass (93%, at station 7).