Physico-chemical parameters play a major role in determining the density, diversity and occurrence of phytoplankton in a headwater stream. The present study was conducted to assess the relationship between physico-chemical parameters and phytoplankton assemblages of Baldi stream of Garhwal Himalayas, India. Results showed an increased concentration in physico-chemical parameters (turbidity, total dissolved solids, nitrates and phosphates) has an adverse impact on the density of phytoplankton during monsoon season at the sampling site S2, where maximum disturbances were recorded. Karl Pearson’s correlation coefficient calculated between physico-chemical parameters and density of phytoplankton revealed that as sediment load increases in the stream, the growth of phytoplankton decreases. Canonical Correspondence Analysis (CCA) between environmental variables and dominant taxa of phytoplankton indicated the influence of physico-chemical parameters on phytoplankton distribution in freshwater ecosystem of Baldi stream of Garhwal Himalayas, India.