In order to investigate the viability of Microcystis vegetative seed stocks and its relationship to harmful algal bloom (HAB) development in Western Lake Erie, sediment samples were collected from different points within the western basin across a two year time period. Sample collection occurred each year in both the fall, just after the initial settling, and in the spring, during recruitment. QPCR techniques identified and quantified both toxic and non-toxic seed concentrations in samples. Spatial and temporal comparisons were accomplished using interpolation tools in ArcMap. Results indicate that not only do vegetative seed stocks vary both spatially and temporally, but that there are clear “hotspots” in seed stock concentrations. In the event that seed stock composition and viability has a strong impact on the temporal and spatial appearance of blooms, further research will determine methods to prevent the recruitment of Microcystis from the seed stocks and consequent HABs development.