Phytoplankton in ice-covered lakes near McMurdo Sound, Antarctica, are stratified vertically in distributions similar to deep chlorophyll maxima commonly observed in lakes and seas. We measured natural fluorcsccnce flux rates, chlorophyll concentration (Chl a), phytoplankton absorption spectra (a,,), photosynthetic efficiency, and spectral irradiance to derive the quantum yields for photosynthesis (+c) and fluorescence (+,). Chlorophyll concentrations predicted from natural fluorescence based on mean ap,, [O.O 15 m2 (mg Chl a) '1 and mean +, [0.044 mol photons lluorcsced (mol photons absorbed)-'1 correlated significantly with measured Chl a (n = 122, r = 0.88). Predictions of primary productivity from natural fluoresccncc based on mean values for +,and a',. were poor. Relationships between 9, : (P, and temperature and between +, : a, and irradiance implied that these environmental variables would not provide good bases for correcting predictions of primary production. +,. : +, varied most coherently with distance from the nutriclinc, due primarily to a large increase in maximum 9,. [0.0015-0.05 1 mol C (mol photons))'] with proximity to the nutricline. Our results indicate that nutrient supply may bc a critical variable to consider when using natural fluorcscencc methods to estimate primary productivity in vertically stable phytoplankton.