The dataset represents the proteome analysis of eight sampling dates during the phytoplankton bloom at the island of Helgoland in the North Sea at the long-term research station ‘Kabeltonne’ (54˚11.3′N, 7˚54.0′E) in 2020. Samples for comparing short-term proteome dynamics were collected for three consecutive days at 7 am and 9 pm on 5th, 6th and 7th May 2020. In addition, long-term proteome changes were analysed using samples collected six days before these samples (29th April 2020, 7 am) and four days after these samples (11th May 2020, 7 am).