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Abstract This work reports the development of a field-deployable and fully handheld fluorometer for environmental water monitoring. Our developed fluorimeter can detect both green algae and cyanobacteria (blue-green algae) while simultaneously differentiating and measuring two different species by selectively measuring chlorophyll a fluorescence from green algae and phycocyanin fluorescence from blue-green algae. As a demonstration, chlorophyll a and phycocyanin photopigments were estimated and differentiated. The system was also tested with an environmental water sample collected from a lake to validate the system functionality. The presented results suggest that our developed fluorimeter could be used as a portable water quality monitoring system for detection of different photopigment of algae.