We conducted a systematic evaluation of the correspondence in fish length data obtained from vertical hydroacoustics and gillnetting across seven European natural lakes differing in abiotic and biotic characteristics. Length data were analyzed as continuous size spectra characterized by their maximum-likelihood estimated exponents b. First, we examined the relationship between size spectra obtained from the two sampling methods. We then examined whether size spectra from the two methods were correlated with lake descriptors separately or in combination. The modeled relationship between the exponents b from the two methods showed that the exponent b from the hydroacoustics was, on average, the same as that from the gillnet sampling in the seven lakes. The exponents b from the hydroacoustics and gillnets, when averaged, were significantly correlated with lake depth, while their differences were significantly correlated with mean air temperature. To conclude, the overall good correspondence between the continuous size distributions obtained by both methods supports the application of vertical hydroacoustics in acquiring size structure of fish communities in lakes, but not in fully replacing the invasive gillnetting. Yet, some specific methodological details require further research.