The effects of continuous chlorination (as NaOCl) on estuarine benthic organisms were investigated with plankton-derived experimental communities. Twelve consecutive studies were conducted, each of which consisted of approximately 60 days colonization periods from flowing estuarine waters continuously receiving nominal 0.00, 0.47, 0.94, or 1.41 mg/liter chlorine produced oxidant (CPO). Compared to controls, short-term (60 day) effects of chlorination included elimination of dominant species, replacement of one dominant species by another, and increased toxic effects correlated with extreme cold weather. Long-term effects (pooled over the 27 month study) included changes in the overall community composition and 40% reduction in numbers of individuals in communities receiving chlorine. Total numbers of species recorded were unaffected by chlorination.