The rapid identification of algae species is not only of practical importance when monitoring unwanted adverse effects such as eutrophication, but also when assessing the water quality of watersheds. Here, we demonstrate a lab-on-a-chip that functions as a compact robust tool for the fast screening, real-time monitoring, and initial classification of algae. The water-algae sample, flowing in a microfluidic channel, is side-illuminated by an integrated subsurface waveguide. The waveguide is curved to improve the device sensitivity. The changes in the transmitted optical signal are monitored using a quadrant-cell photo-detector. The signal-wavelets from the different quadrants are used to qualitatively distinguish different families of algae. 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 networks designed for the real-time field analysis of cells and microorganisms.