Colonization patterns and community changes in benthic macroinvertebrates in the Cheonggye Stream, a functionally restored stream in downtown Seoul, Korea, were studied from November 2005 to November 2007. Benthic macroinvertebrates were quantitatively sampled 15 times from five sites in the stream section. Taxa richness (59 species in total) increased gradually over the first year, whereas the density revealed seasonal differences with significantly lower values in the winter season and after flood events. The benthic macroinvertebrate fauna may have drifted from the upstream reaches during floods and from the Han River, arrived aerially, or hitchhiked on artificially planted aquatic plants. Oligochaeta, Chironommidae, Psychodidae, and Hydropsychidae were identified as major community structure contributors in the stream. Swimmers and clingers colonized relatively earlier in the upper and middle reaches, whereas burrowers dominated particularly in the lower reaches. Collector-gatherers colonized at a relatively early period throughout the stream reaches, and collector-filterers, such as the net-spinning caddisfly (Cheumatopyche brevilineata), predominated in the upper and middle reaches after a 1-year time period. Cluster analyses and multi-response permutation procedures demonstrated that the Cheonggye Stream shares more similarities with the Jungnang Stream than with the Gapyeong Stream. Detrended correspondence analysis and nonmetric multidimensional scaling demonstrated that physical environmental factors (depth, current velocity, dissolved oxygen, and pH) as well as nutrients (total nitrogen and total phosphorous), water temperature, and conductivity could affect the distribution of benthic macroinvertebrates in the study streams.