With 33 years of phytoplankton quantitative studies carried out, a series of qualitative data with a length of over 80 years is at our disposal. About 500 algal species have been found in plankton by different researchers. In different seasons and years 35 main species (dominants and subdominants) form 68–96 % of biomass in L. Pihkva (southern, more eutrophic part) and 60–97 % in L. Peipsi (northern, less eutrophic part). L. Lammijarv, connecting the two parts is similar to L. Pihkva in respect to phytoplankton and the trophic state. Diatoms and blue-green algae prevail in biomass, diatoms and green algae, in the species number. The oligo-mesotrophic Aulacoseira islandica (O. Muller) Sim. is characteristic of the cool period; A. granulata (Ehr.) Sim. and Stephanodiscus binderanus (Kutz.) Krieger prevail in summer and autumn, the latter being most abundant in the southern part. Gloeotrichia echinulata (J.S. Smith) P Richter and Aphanizomenon flos-aquae (L.) Ralfs dominate in summer causing water-bloom. Phytoplankton has mostly three maxima in seasonal dynamics in L. Peipsi and two in L. Pihkva. Its average biomass in spring in different years has fluctuated in the range 5.6–16 and 6–12.7 g m−3, in summer 3.1–14.8 and 5.6–125 (10–20 in most cases); and in autumn 7–16.3 and 5.2–26 in the northern and southern parts, respectively.