Short-term changes in temporal and spatial distributions of the toxic cyanobacterium Planktothrix rubescens in Lake Zurich were investigated using high-resolution data sets acquired with an autonomous surface vessel (ASV). Data profiles were recorded with a multi-parameter probe while the ASV navigated along 1.5 km toward a waypoint located on the other side of the lake by using a global positioning system. We deployed the ASV seven times on five consecutive days during the stratification period (July 2011) to generate cross-sectional views of temperature, light, oxygen, and phycoerythrin and chlorophyll fluorescence from surface to 18 m. The data were also used to compute daily photosynthetic rates. Data showed a daily reshaping of the P. rubescens distribution in the metalimnion on both horizontal and vertical axes, from patches to a shore-to-shore spreading. A thermocline depression observed after 16 h of sustained winds forced the accumulation of P. rubescens on the downwind shore. The compression of the metalimnion and its downward shift by 6 m within 24 h suggested the modulation of a longitudinal seiche following the wind event. This passive transport of the metalimnetic P. rubescens population resulted in a 90% light reduction, and a decrease of the averaged daily photosynthetic rate from +21 mmol O2 m−2 d−1 to −10 mmol O2 m−2 d−1. Negative photosynthetic rates were computed on 2 d out of 5 d, meaning that the transport of P. rubescens by seiches significantly affected the balance between oxygen production and utilization in Lake Zurich, especially because it is the dominant primary producer.