► We compared two common survey methods of aquatic macrophytes in boreal lakes. ► More taxa in less time were found with a phytolittoral inventory (PI) than with a transect survey (TS). ► Metrics of taxonomic composition varied more by method than did a trophy-specific index. ► The methods did not differ in relation to among-observer variation. ► The PI method is recommended for biodiversity surveys and the TS for ecological status assessments. To compare the performance of two common methods for surveying boreal lake aquatic macrophyte communities (the transect survey and the phytolittoral inventory) in lake bioassessment, we studied five small humic lakes with both methods. In addition to this pairwise comparison, we contrasted available independent sets of reference lake data of either methodological origin. Specifically, we compared the observed species richness and a number of ecological quality (community) metrics and their variability both between the methods and within them in relation to sampling effort and operator. With the phytolittoral inventory, more taxa (mean 38.8±s.d. 12.1) were observed than with transect survey (29.8±6.5) in a shorter time. Ecological quality metrics relying on taxonomic composition were sensitive to variation both between (reference lake data: t-test, p<0.001) and within methods (metric values varied with sample size), whereas a trophy-specific metric based on indicator species was more robust in this respect (ref. lakes: t-test, p=0.788; minor variation with sample size). The two methods did not differ in among-observer variation (CV of community metrics 5.0–8.7), which was, as indicated by an NMDS ordination, relatively low compared to among-lake variation. Overall, the results highlight the importance of establishing reference conditions using unified methods, which are also consistent with those used in the macrophyte-based ecological assessments. Even though the more cost efficient phytolittoral inventory method is more suitable for biodiversity surveys focusing on the overall species richness and rare species, we suggest that the transect survey better meets the requirements of ecological status assessment, as it produces information also on the zonation of the littoral vegetation.