Monitoring programs for harmful algal blooms (HABs) typically rely on time-consuming manual methods for identification and enumeration of phytoplankton, which make it difficult to obtain results with sufficient temporal resolution for early warning. Continuous automated imaging-in-flow by the Imaging FlowCytobot (IFCB) deployed at Port Aransas, TX has provided early warnings of six HAB events. Here we describe the progress in automating this early warning system for blooms of Karenia brevis. In 2009, manual inspection of IFCB images in mid-August 2009 provided early warning for a Karenia bloom that developed in mid-September. Images from 2009 were used to develop an automated classifier that was employed in 2011. Successful implementation of automated file downloading, processing and image classification allowed results to be available within 4 h after collection and to be sent to state agency representatives by email for early warning of HABs. No human illness (neurotoxic shellfish poisoning) has resulted from these events. In contrast to the common assumption that Karenia blooms are near monospecific, post-bloom analysis of the time series revealed that Karenia cells comprised at most 60-75 % of the total microplankton.