We demonstrate a small device with a microfluidic channel and an integrated waveguide that functions a compact rudimentary tool for the detection, real-time monitoring, and potentially classification of algae. In order to reduce parasitic noise the micro-device used a curved subsurface optical waveguide to illuminate particles transiting through a microfluidic channel. The changes in the transmitted signal are monitored using a quadrant-cell photo-detector. The signals wavelets from the different quadrants are used to qualitatively distinguish different families of algae. Additional information, such as flow direction, is also provided. The channel and waveguide are fabricated out of a monolithic fused-silica substrate using a femtosecond laser-writing process combined with chemical etching. This proof-of-concept device paves the way for more elaborate femtosecond laser-based optofluidic micro-instruments incorporating waveguide network designed for the real-time analysis of cells and microorganisms in the field.