The early detection of changes in the level and composition of algae is essential for tracking water quality and environmental changes. Current approaches require the collection of a specimen which is later analyzed in a laboratory: this slow and expensive approach prevents the rapid identification of changes in algae species dynamics and hinders a quick response to potential outbreaks. In a recent work, we presented a microfluidic chip for classifying and quantifying algae species in water. Here, we study the device performance and specifically compare the difference in results obtained by using a discriminant analysis classification approach and a neural network pattern recognition approach. Using both of these methods, we demonstrate the classification of algae by species, of microspheres by size, and of a detritus/cyanobacteria mixture by type. In each of the demonstrations here, the neural network outperforms the discriminant analysis method.