Between 1990 and 2001, late-winter phytoplankton blooms were common in parts of the lower Great Lakes (southern Lake Michigan, Saginaw Bay and southern Lake Huron, and western Lake Erie), providing resources for over-wintering Zooplankton. In Lake Michigan up to 2001, detailed remote sensing and ship studies documented well-developed late-winter blooms in the southern gyre (circular bloom termed the ‘doughnut’). However, from 2001 to 2008, the winter blooms in Lake Michigan also supported early season veliger larvae from the introduced, cold-water adapted “profunda” morph of quagga mussels (Dreissena rostriformis bugensis). Remote sensing and ship studies revealed that settled mussels caused an extraordinary increase in water transparency and a simultaneous decrease of Chl a in the late-winter bloom. Before quagga mussels in 2001, water transparency was 74–85% at deep-water sites, whereas it increased progressively to 89% by 2006 and 94–96% by 2008. Chlorophyll a concentrations in the gyre rings were 1.1–2.6 µg/L in 2001, declining to 0.5–1.7 µg/L by 2006 and 0.4–1.5 µg/L by 2008. The reduction of Chl a in the winter bloom rings from 2001 to 2008 was 56–78% for the western limb and 74–75% for the eastern limb. Zooplankton species abundance, composition and abundance also changed, as cyclopoid copepods became very scarce and overwintering omnivorous calanoid copepods declined. Reduction in late-winter phytoplankton and Zooplankton poses a serious threat to open-water food webs.