This system was developed to aim for offering water and aquaculture industries a rapid, precise, and low-cost method to detect cyanobacteria, cyanotoxins, and taste and odor compounds in water and aquaculture products. An AI-based image recognition cell-phone APP has been developed to near-real-time identify harmful cyanobacteria in water, using image taken from a low-cost handheld microscope. An immunoassay test kit was developed for the rapid determination of cyanotoxins and T&O compounds. Seven biomolecular analytical kits and a database were developed to quantify the functional genes for cyanotoxins and T&O compounds. The data obtained serve as the benchmarks for water-relevant industry managers to determine their response actions and to secure the quality of their water and products.This is the first system with the capacity of on-site determination of harmful cyanobacteria and their metabolites using multiple technical approaches. With the integration of AI-based image recognition method, inexpensive handheld microscope, and a cell-phone based APP, and immunoassay test kit, the system is able to on-site and rapidly identify harmful cyanobacteria and their metabolites. The technology developed to offer a low cost, non-labor intensive approach for water and aquaculture industries to quickly and easily evaluate the risk of their water quality and aquaculture products. The multiple technologies based system has been successfully tested in more than 35 different water bodies in Taiwan and Asia, proving that this system can be applied in different regions in the world.The developed system offers a cheaper, faster, and tiered approach for the water reservoir and utilities and aquaculture industry to evaluate their cyanobacteria-relevant water and product quality. It can also be applied in wastewater treatment and water recycled plants. The potential users of the system include hundreds of reservoirs and water utilities and thousands of aquaculture farms in Taiwan, and more than 10,000 water utilities and 10,000 aquaculture farms in Asia.