Recovery rates of different metrics (physiological, biological), trophic levels (phytoplankton, invertebrate consumers), and habitats (pelagic, benthic) were studied over a 16-y period in 10 boreal lakes recovering from acidification. Several of the metrics showed significant, positive trends over time that supported our expectations of biological recovery. Taxonomic diversity of phytoplankton assemblages, but not assemblage composition, showed early signs of recovery that were strongly related to increases in pH in both reference and acidified lakes. Results from benthic invertebrate assemblages were, however, equivocal. Littoral invertebrate taxon richness and diversity increased in both acidified and reference lakes, whereas sublittoral and profundal invertebrate assemblages of both lake groups showed clear negative trends. These findings indicate that sublittoral and profundal assemblages might be influenced by factors other than lake acidity, such as coincident changes in habitat quality (e.g., ambient O₂ and temperature). Our findings show that the selections of the group of organisms to monitor recovery and the habitat in which to monitor recovery must be considered carefully when designing and implementing programs to assess degradation and recovery.