The occurrence and intensity of (harmful) algal blooms (HABs) have increased through the years due to rapidly changing environmental conditions. At the same time, the demand for low-cost instrumen-tation has increased substantially, enabling real-time monitoring and early stage detection of HABs. To meet this challenge, we have developed a compact multi-wavelength fluorometer for less than 400 USD. This is possible by using readily available, low-cost optical and electronic components. Its modular design results in a highly versatile and flexible monitoring tool. The algae detection module enables a continuous identification and control of relevant algal groups based on their spectral charac-teristics with a detection limit of 10 cells/L. Besides its usage as a benchtop module in the laboratory, the algae module has been integrated into submersible housings and applied in coastal environments. During its first in situ application in the Port of Genoa, seawater samples of mixed algal composition were used to demonstrate the successful discrimination of cyanobacteria and dinophytes as well-known toxin producing classes. The fabrica-tion, operation and performance as well as its first in situ application are addressed.