Veraval, one of Asia's largest fishing harbours, situated on the south-west coast of Gujarat, India, has transformed into an industrial hub dominated by fish processing units, rayon manufacturing industry, and transportation facilities. The study investigated the high abundance of Tetraspora gelatinosa along with the augmented level of ammonia in the harbour. The high concentration of ammonia was associated with the accumulation of sewage, industrial, and fishery wastes in the harbour. Low-energy expenditure associated with assimilation of ammonia made it a principal nitrogen source for Tetraspora gelatinosa growth. Even though ammonia is the preferred nitrogen source by phytoplankton, elevated concentration causes toxicity to the cells. Augmented level of ammonia and high TSS hampered the efficiency of PS II, thereby impeding the chlorophyll a degradation and oxygen evolution. Built of the organic load from fish processing industries as well as domestic waste along with a reduction in photosynthetic oxygen evolution has made the harbour hypoxic (DO < 1.6 mg L)/anoxic (DO = 0.0 mg L). Shannon-Wiener diversity index as a pollution index suggested that the inner harbour area was highly polluted as the diversity ranged from 0.01 to 1.57. Whereas, the outer harbour (Near-shore and off-shore) with less anthropogenic effect recorded high diversity (av. 2.17) suggesting a healthy environment.