We compared the within- and among-lake variability of benthic communities in small, near-pristine lakes vs lakes affected by nonpoint-source pollution in southern Finland. We used 2 sampling methods, profundal grab sampling and the chironomid pupal exuvial technique (CPET), and compared the signal-to-noise ratios (S/N) of the 2 data sets. We also assessed lake condition using the benthic quality index, identified macroinvertebrate taxa indicative of different trophic conditions, and evaluated the concordance of species ordinations obtained using the 2 collection methods. Both data sets discriminated effectively among the lake groups, and the 2 community ordinations were significantly concordant. The number of chironomid species in the CPET samples was higher than the total number of macroinvertebrate taxa found in the profundal grab samples, and the CPET method appeared more efficient than profundal grab sampling at detecting profundal taxa. Despite the slightly stronger signal strength of the profundal grab samples, randomization tests showed that only the CPET data had S/N significantly higher than expected by chance. CPET data also better reflected the trophic status of the lakes. Indicator species analysis showed that 7 chironomid taxa and Pisidium spp. (Sphaeridae) indicated good water quality, whereas 5 chironomid species and the phantom midge Chaoborus flavicans indicated impacted conditions in these lakes. Our results suggest that CPET might be more efficient than profundal grab sampling for describing the chironomid fauna and the ecological status of small mesohumic lakes, and it should be considered as an alternative or supplementary assessment tool to more traditional methods.