Interannual variation in proportion of left-sided individuals has been studied in the populations of the European flounder from Onega (2002–2019), Mezen (2010–2016), and Dvina (2005–2019) bays of the White Sea. It was found that the flounder populations show no statistically significant and consistent changes in this character. The frequency of left-sided individuals in the local populations and the character of interpopulation differences in different years of the observation period remain relatively constant. The comparison of the results of this study with those of earlier studies reveals a similarity in proportions of left-sided fish over the past 40–60 years in flounder populations of the Kandalaksha Bay and Onega Bay. These results highlight the importance of the proportion of left-sided morphs for the analysis of population differentiation of the European flounder in the White Sea.