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Planktonic organisms including phyto-, zoo-, and mixoplankton are key components of aquatic ecosystems and respond quickly to changes in the environment, therefore their monitoring is vital to follow and understand these changes. Advances in imaging technology have enabled novel possibilities to study plankton populations, but the manual classification of images is time consuming and expert-based, making such an approach unsuitable for large-scale application and urging for automatic solutions for the analysis, especially recognizing the plankton species from images. Despite the extensive research done on automatic plankton recognition, the latest cutting-edge methods have not been widely adopted for operational use. In this paper, a comprehensive survey on existing solutions for automatic plankton recognition is presented. First, we identify the most notable challenges that make the development of plankton recognition systems difficult and restrict the deployment of these systems for operational use. Then, we provide a detailed description of solutions found in plankton recognition literature. Finally, we propose a workflow to identify the specific challenges in new datasets and the recommended approaches to address them. Many important challenges remain unsolved including the following: (1) the domain shift between the datasets hindering the development of an imaging instrument independent plankton recognition system, (2) the difficulty to identify and process the images of previously unseen classes and non-plankton particles, and (3) the uncertainty in expert annotations that affects the training of the machine learning models. To build harmonized instrument and location agnostic methods for operational purposes these challenges should be addressed in future research. [ABSTRACT FROM AUTHOR]