Spatial and temporal variations in surface water phytoplankton pigment distribution in the Bay of Bengal were studied during the spring intermonsoon (SpIM, February–April) and the commencement of the summer monsoon (CSM, May–June), using pigment and diagnostic indices. The Prokaryotic pigment index (Prok DP) was dominant at all the oceanic stations whereas the Flagellate pigment index (Flag DP) was dominant at the near coastal stations. However, during the commencement of summer monsoon, an oscillation in the dominance of Prok DP and Flag DP was observed in the central oceanic bay, whereas flagellates and diatoms were dominant at the near coastal stations. This change in pigment pattern is possibly related to the influence of rainfall. Comparison of pigment data with microscopic cell counts indicated a significant relationship between the diatom pigment index (Diat DP) and diatom abundance. However, the relationship between the dinoflagellate pigment index (Dino DP) and dinoflagellate abundance was not significant. Studies coupling pigment composition analysis with microscopic analysis of phytoplankton in natural conditions should thus be a prerequisite in establishing valid biogeochemical and ecosystem models.