Increasing water clarity in Lake Ontario has led to a vertical redistribution of phytoplankton and an increased importance of the deep chlorophyll layer in overall primary productivity. We used in situ fluorometer profiles collected in lakewide surveys of Lake Ontario in 2008 to assess the spatial extent and intensity of the deep chlorophyll layer. In situ fluorometer data were corrected with extracted chlorophyll data using paired samples from Lake Ontario collected in August 2008. The deep chlorophyll layer was present offshore during the stratified conditions of late July 2008 with maximum values from 4–13 μg l⁻¹ corrected chlorophyll a at 10 to 17 m depth within the metalimnion. Deep chlorophyll layer was closely associated with the base of the thermocline and a subsurface maximum of dissolved oxygen, indicating the feature's importance as a growth and productivity maximum. Crucial to the deep chlorophyll layer formation, the photic zone extended deeper than the surface mixed layer in mid-summer. The layer extended through most of the offshore in July 2008, but was not present in the easternmost transect that had a deeper surface mixed layer. By early September 2008, the lakewide deep chlorophyll layer had dissipated. A similar formation and dissipation was observed in the lakewide survey of Lake Ontario in 2003.

Phosphorus loading declined between the 1970s and the 1990s, leading to oligotrophication of the offshore waters of Lake Ontario during that time period. Using lake-wide data from the intensive field years of 2003 and 2008 and from available long-term data sets on several trophic state indicators (total phosphorus [TP], soluble reactive silica [SRSi], chlorophyll a and Secchi disc transparency [SDT]), we tested the hypothesis that oligotrophication of the offshore waters of Lake Ontario has continued in the 2000s. Significant differences between 2003 and 2008 include higher spring (April) TP, SRSi, and SDT in 2008, lower summer (July–August) SDT in 2008, higher summer chlorophyll a in 2008, and lower fall (September) TP, SRSi, and chlorophyll a in 2008. The decline in SRSi from spring to summer was greater in 2008 than in 2003. Change point and regression analyses on the long-term data revealed no trend in spring TP since 1996, in summer chlorophyll a since 1994, in spring SDT since 1998, in spring SRSi or SRSi decline from spring to summer since 1999, or in summer SDT since 2001. Neither the comparison of the 2003 and 2008 surveys nor the analysis of the long-term data supported our hypothesis of continued oligotrophication of the offshore of Lake Ontario in the 2000s.

Mysids are an important component of Great Lakes foodwebs, both as a prey for fish and as a predator on zooplankton. We monitored mysid abundance in Lake Ontario using lake-wide hydroacoustics data and vertical net hauls collected 1–5 August 2008 during the Ontario Ministry of Natural Resources and New York State Department of Conservation forage fish survey. Acoustic volume backscattering strength was highly correlated with both density and biomass of mysids although the correlation with biomass was stronger. The slopes of these relationships were not significantly different from theory (0.10) indicating a linear relationship between abundance and backscattering strength. Size structure significantly affected the relationship between backscattering strength and density but not between backscattering strength and biomass. Average target strength for areas with small mysids was −91.9 dB per mysid, and in areas with both small and large mysids it was −88.2 dB per animal. Acoustic estimates for Lake Ontario calculated with these regressions provided a lake-wide estimate weighted by lake area within depth intervals, of 228 mysids m⁻² (CV 17.6%) and 0.93 g dw m⁻² (CV 12.9%). Density and biomass in 14 net hauls averaged 316 mysids m⁻² (range 0 to 1113) and 1.35 g dw m⁻² (range 0 to 3.89). Mysid biomass was 33% of the biomass of other crustacean zooplankton in the summer of 2008. As in 2005, areas of low mysid abundance were detected in the middle of the transects and along the north shore. Lakewide mysid abundance in the summer of 2008 was higher than in a similar acoustic survey in the summer of 2005 and in whole-lake autumn 2000–2007 net surveys, suggesting that mysids are persisting in Lake Ontario and abundant relative to other Great Lakes.