Recent increases in global urea usage, including its incorporation in slow-release fertilizers commonly used in lawn care in Florida, have the potential to alter the form and amount of nitrogen inputs to coastal waters. This shift may, in turn, impact phytoplankton community diversity and nutrient cycling processes. An autonomous water quality monitoring and sampling platform containing meteorological and water quality instrumentation, including urea and phycocyanin sensors, was deployed between June and November of 2009 in Sarasota Bay, Florida. This shallow, lagoonal bay is characterized by extensive and growing urban and suburban development and limited tidal exchange and freshwater inputs. During the monitoring period, three high-biomass (up to 40 µg chlorophyll-a·L−1) phytoplankton blooms dominated by picocyanobacteria or picoeukaryotes were observed. Each bloom was preceded by elevated (up to 20 μM) urea concentrations. The geolocation of these three parameters suggests that “finger canals” lining the shore of Sarasota Bay were the source of urea pulses and there is a direct link between localized urea inputs and downstream picoplankton blooms. Furthermore, high frequency sampling is required to detect the response of plankton communities to pulsed events.