Phytoplankton biomass, composition, and size structure were examined in oligotrophic Kootenay Lake, British Columbia, during two years of a fertilization program aimed at enhancing declining stocks of kokanee salmon. Phosphorus (47.1 metric tonnes per year) and nitrogen (206.7 metric tonnes per year) were added to the northern end of this long, narrow lake. Comparisons were made between the fertilized North Arm and unfertilized South Arm of the lake. The two arms did not indicate any significant differences in water chemistry prior to fertilization. Algal biomass was highest at the fertilized sites during the spring bloom (June) but did not differ between fertilized and unfertilized regions during the summer months (June 21 – September 21). There was an overall increase in biomass from 1992 (the first season of experimental nutrient loading) to 1993. Algal composition at the division level did not change between fertilized and unfertilized sites, except in 1993 when an increase in summer Chlorophyta was seen at the fertilization area relative to the unfertilized area. Diatoms dominated the phytoplankton community followed by Cryptophyta and Chrysophyta. The biomass of the nanoplankton (2 to 20 μm) and microplankton (20 to 64 μm) size fractions was not altered between fertilized and unfertilized sites in 1992, but there was an increase in net plankton (> 64 um) at the fertilized sites. In 1993, the average biomass of the nanoplankton had decreased at both sites while average microplankton biomass was significandy higher than in 1992. Photosynthetic picoplankton (0.2 to 2 μm) biomass was lower in the fertilized than in die unfertilized area on the one date of assessment in the summer of 1993, suggesting that fertilization may be shifting die energy flow in Kootenay Lake towards a more efficient classical food chain.