Shallow coastal regions face heightened vulnerability due to human development, making them susceptible to substantial influxes of human-caused inputs alongside waters with low pH levels. This research delved into a microcosm pH alteration experiment to explore the impact of pH reduction on the generation of bioactive substances by marine phytoplankton in the eutrophic coastal waters of the Bay of Bengal. Initially, the prevalent compounds in the surface seawater were fucoxanthin at 75%, zeaxanthin at 10%, and other bioactive elements like diadinoxanthin, diatoxanthin, and β-carotene collectively contributing to around 15%. Notably, all bioactive compounds and Chl-a concentrations significantly favored the control container (ranging from 35–70%), while the least growth occurred in the more acidified experimental containers (15–40%). In alignment with the above findings, the nutrient uptake rates were comparably diminished in the acidified experimental containers compared to the control group. The ratio between protective bioactive compounds (Diato + Diadino + Zea + β-Car) and synthetic bioactive compounds (Fuco + Chl-a) varied from 0.03 to 0.8, with the control container exhibiting the lowest values, and the more acidified experimental containers displaying the highest values of significance. Similarly, the DT index (diatoxanthin / (diatoxanthin + diadinoxanthin)) ratios followed a parallel pattern, with the control container showing the lowest average ratios and the acidified experimental containers displaying the highest ratios. Furthermore, based on our current study, we postulated that acidified water stimulates the proliferation of carotenoid-based bioactive compounds in marine regions more prominently than their synthetic counterparts. Mainly, the production of bioactive compounds in these experiments could also be influenced by our acidification method.