In coastal and abiding zones, ground water continuously facing very slight but alarming increasing trend in salinity due to several reasons such as its excess loss or use, with constant dissolve of salts from earth surface and heat-trapping pollution from human activities, rising sea levels and finally high flooding. Many recent studies indicate such slight elevation in ground water salinity that may as insults to the fresh water inhabitants, was the driving force, to comprehensively investigate the effects of low salinity stress on the coastal zone fresh water inhabitants. The present study was aimed to carefully investigate the effects of sub-lethal salinity on multiple aspects such as the growth pattern, morphometric changes, haematological alternation, altered histology and generation of oxidative stress in different tissues of Heteropneustes fossilis, a hardy fish model. Fishes were exposed to sub-lethal salinity i.e. 3, 6 and 9 ppt for 45 days against a control set (tap water, ~0 ppt) under constantly monitored pH, temperature, dissolved oxygen and alkalinity. Correlation and discriminant function analysis indicate that sub-lethal salinity acts as a strong modulator in fish physiology. Decline in the studied parameters such as gain in body weight, feed intake and morphometry in higher salinities was confirmed which finally attributed to decline in the growth of the fish. Significant loss in haemoglobin content, RBC count and eosinophils was coupled with amelioration in neutrophil count at higher salinities of 6 and 9 ppt. Normal histo-architecture was also lost in the fish, might be due to the generated oxidative stress levels and/or osmotic imbalances in the accessory respiratory organ, brain, liver, gill and muscle tissues of the fish. Therefore, loss of compromised normal physiology due to the toxic effects of low salinity in the inhabitants including hardy fishes under changing climatic conditions (that leads to increase the ground water salinity) alarms about maintaining fresh water quality in coastal and allied zone globally in coming decades.