The persistence and stability of invertebrate communities of three benthic habitats (littoral, sublittoral, profundal) over 16 years were compared between minimally disturbed (reference) and disturbed (acidified) boreal lakes. No significant differences were found for either persistence or stability and degree of disturbance, although clear differences in community composition existed between the two lake groups. Differences in mean persistence and stability were found between the three benthic habitats. Profundal habitats showed the highest and littoral habitats the lowest community persistence and stability. Correlation of both metrics with water chemistry and the NAO winter index showed generally negative relationships with climate and pH, but positive relationships with water color (minimally disturbed) and TOC (acidified). Littoral invertebrate assemblages had lower persistence and stability compared to invertebrate assemblages in environmentally more simple habitats such as the profundal. Our results support the idea that complex habitats having high interannual variability are less suitable for monitoring due to the high probability of not detecting change if/when it occurs. These findings have strong implications for the design of lake bioassessment programs, emphasizing the importance of habitat stratification.