Abstract An eigenvalue analysis of the vertical phytoplankton biomass equation is applied to calculate the differential sinking- and loss-rates of phytoplankton for different taxonomic groups in Lake Lyndon B. Johnson (LBJ) (Texas) and in Lake Erie. The analysis includes factors determining the phytoplankton composition, including losses due to turbulent mixing and to sinking, and a death-term to account for endogenous decay and predation. Gross growth-rates were obtained from community and individual 14C production data (autoradiography) and from biomass measurements. Green algae produced the largest gross growth-rates, 1–1.75 d −1, and the largest calculated sinking-rates, 1–3 m d −1. The lowest gross growth-rates (< 0.5 d −1) and sinking-rates (< 0.1 m d −1) were determined for blue-green algae and phytoflagellates, while diatoms were intermediate, with growth-rates generally in the range 0.25–0.75 d −1 and calculated sinking-rates of 0.1–1.0 m d −1.