This paper reports on an investigation of the capability of the bbe Moldaenke Fluoroprobe instrument for distinguishing major algal taxa. It employs a Department of Fisheries and Oceans database of Fluoroprobe data collected simultaneously with water samples later analyzed for chlorophyll fluorescence, various water quality parameters and algal taxonomy, between August and September/October 2003. The Fluoroprobe measures fluorescence at six excitation wavelengths and records both raw fluorescence intensity and estimated chlorophyll biomass concentrations of four major algal taxa. Multiple regression of the fluorescence data explains 63% of variance in chlorophyll a in samples, and predicts chlorophyll a with a root mean square error of 7% of the range of concentrations characteristic of Lake Winnipeg. Bacillariophytes and cyanophytes dominate the algal community in Lake Winnipeg, the former characteristically dominant in spring and late autumn, and the latter from midsummer through to early autumn. Multiple fluorescence successfully distinguishes and predicts bacillariophyte and cyanophyte biomass with similar success, i.e. r2 = 0.68 in both cases, although with a larger relative RMSE, at best 10% and 19% of the range in Lake Winnipeg, respectively. It is only a weak predictor of cryptophyte biomass, a subdominant group in Lake Winnipeg except at very low concentrations, and a weaker predictor of chlorophyte biomass, also a sub -dominant group in the lake. Nonetheless, by use of multiple regressions developed from the paired data set, we were able to successfully reproduce the seasonal patterns determined by microscope counts, of both dominant and subdominant groups through a mid -summer to late autumn period in 2003.