Understanding and monitoring aquatic biodiversity is critical for ecological health and conservation efforts. This paper proposes SuoiAI, an end-to-end pipeline for building a dataset of aquatic invertebrates in Vietnam and employing machine learning (ML) techniques for species classification. We outline the methods for data collection, annotation, and model training, focusing on reducing annotation effort through semi-supervised learning and leveraging state-of-the-art object detection and classification models. Our approach aims to overcome challenges such as data scarcity, fine-grained classification, and deployment in diverse environmental conditions.