Methods for in situ detection and classification of analyte within a fluid sample are provided. In one embodiment, the method can include: (a) continuously flowing the fluid sample through a multivariate optical computing device, wherein the multivariate optical computing device illuminates an area of the fluid sample as it flows through the multivariate optical computing device to elicit a continuous series of spectral responses; (b) continuously measuring the series of multivariate spectral responses as the fluid sample flows through the multivariate optical computing device; (c) detecting an analyte (e.g., phytoplankton) in the sample based on an multivariate spectral response of the plurality of spectral responses; and (d) classifying the analyte based on the multivariate spectral response generated by the analyte.