Sediments were dated and the quality assessed by polyphasic approach in an area of Lake Saimaa, which has received waste water from bleached kraft pulp production since 1954. The chosen nonrecipient forest Lake Pyylampi was situated in the same area. The activities of the enzymes butyrate-esterase and aminopeptidase were depressed at the depth of 2 to 8 cm in the recipient but not in the forst lake sediment. In the same layers the contents of EOX-C1 and toxicity to Vibrio fischeri were very high compared to those above or below. Toxicity to microbial community in the 2 to 8 cm layer was also indicated by a gap in the ATP content and a drop in diatom species richness from the 70 species to < 50 reflecting decreased water quality of the pelagic area. All these changes dated to the period of heavy organic halogen discharges, from 1960 to late 1980s, which led to sediment accumulation of solvent soluble halogen at a depth of 2 to 8 cm, to 6.4 g m−2 (cm)−1. In the most polluted sediment layers heavy metal accumulation was too little to be related to the toxicity of these layers. Almost complete recovery of both the sediment microbial ecosystems and of the pelagic diatoms occurred after elemental chlorine was completely substituted by chlorine dioxide and biological treatment adopted for wastewaters. Butyrate-esterase and aminopeptidase, but not phosphatase, activities correlated positively with the ATP content of the sediment. Butyrate-esterase may be used as a tool to estimate microbial biomass.