Nanophytoplankton, the key component of algal communities, remains understudied, thus there is a substantial knowledge gap about dynamics of abundance, biovolume, and cell size of specific algae. Here, I studied weekly changes in abundance, biovolume, cell volume, and cell surface to volume (SV) ratio (> 11,700 cells measured) of specific nanophytoplankton groups using amplicon sequencing and catalyzed reported deposition‐fluorescence in situ hybridization. I applied oligonucleotide probes to study major nanophytoplankton groups: chlorophytes, chrysophytes, pelagophytes, cryptophytes, pedinellids, and haptophytes. I designed three novel probes, two for pedinellid species Apedinella radians and Pseudopedinella elastica, and for a haptophyte genus Haptolina. Chlorophytes were the most abundant group, followed by haptophytes and cryptophytes. Abundance and biovolume of specific groups showed distinct seasonal dynamics and fluctuated up to 100‐fold within a week. Different groups contributed to nanophytoplankton peaks over the season, and this pattern was consistent down to a genus/species level, as shown for cryptophytes, pedinellids, and haptophytes. Inorganic nutrients were the best explanatory variables for abundance and biovolume, but their importance varied for specific groups. Thus, the differences in seasonal dynamics of different algal groups can be explained by temporal niche separation between them. Changes in nanophytoplankton size structure were substantial, and cell volume varied over 104‐fold. However, the size dynamics (variability in cell volume and SV ratio) was lower at genus/species level, indicating changes in nanophytoplankton size structure likely resulted from changes in community composition. Temperature and nutrients best explained the size dynamics, but their explanatory power differed for specific nanophytoplankton groups.