Keenjhar lake of Sindh, Pakistan, second largest natural freshwater lake had a rich flora of submerged, floating and emergent aquatic plants and it was also rich in the fish on which live hood of local communities mainly depended on the resources. The lake is also very important for the Karachi Water and Sewerage Board, as it is the only source that provides drinking water to 1.8 million people of the city. Besides being the main water supply source, the lake is also considered to be an important site for breeding and a passageway for water birds that migrate to Pakistan in winter from Russian Siberia and other cold countries. The highly contaminated industrial effluent, which comprises of very toxic waste from hundreds of industrial units of Kotri and Noori abad, is being discharged in the lake without proper treatment. It is responsible to increases different type of organic and inorganic contaminates, that persistent in the lake and cause serious damage in the physico-chemical parameters of lake water. The pollution of lake in 2011 was also addressed by supreme court of Pakistan due to severe contaminates burden. This research project comprises an analysis of some important biophysical and biochemical parameters of fish species Notopterus notopterus collected in the duration of three years to check the toxicity level of fluoride contaminate and their effects on fish community. Fluoride was selected as a major inorganic persistent contaminate of aquatic resources, univalent poisonous gaseous halogen, the most chemically reactive and electronegative of all the elements of Periodic Table, readily oxidizes the many organic compounds. Fish were collected in the months of February and March from 2008-2010.Weight and length of the fish was recorded after the collection from the lake. After collection fish were kept in tap water (receiving from the same lake in Karachi city for drinking purpose) in laboratory for two months and two doses (1.5 and 3 g /70 L in each aquarium) of fluoride was administrated in two separate fish aquariums while one was taken as non-treated (control). The weight and length of the fish were monitored at two different dose (1.5 & 3.0 g/70 L) of NaF. It showed significant decline during the time interval of 24,48, and 72h with different mortality rate in each year. The time interval of 24h, 48h and 72h wereselected after analysis of different parameters at variable time intervals, it was observed that marked effect on biochemical constituents were observed significantly in this duration and after this no significant changes showed that initial administration of fluoride concentration was crucial. All physical parameters of the site of collection including temperature of the water, humidity of the air were noted. An astonishing thing was observed related to that of temperature and humidity at Lake Site that the temperature of the lake was high and humidity was low during the same months of collection in year 2009 and 2010 with reduced length and weight of same fish under investigation as compared to 2008. Physioco-morphological variations were observed related to applied dose on whole fish body.The skin becomes black with turned scale, weakness in movement of fish, eye vision was affected, and mouth of fish was stuck. Dissection of the fish showed that all main organs were dissolved while heart, liver, kidney were not visualized in the body at the time of mortality in fluoride treated fish which was different for each year. The lowest time of mortality was observed in the fish collected in year 2010 (45 d) showed burden of contaminant in lake while it was maximum (90d) for 2008 collections at both doses.As a matter of fact that approximately all chemical reaction in a living cell requires enzymes in order to occur at speed enough for sustaining life. Results showed that enzyme activity was a good environmental biomarker of pollution pressure. Alterations in enzymes profile are important pollution indices. Alteration in enzymes activity may be related with the muscles morphology and physiology.Cell membrane permeability lets the enzymes leaching or decrease membrane permeability allows it to accumulate in cell. Cellular damage is another major cause of decrease or increase in enzyme activity result in the inhibition of carbohydrate- protein metabolism. Three key enzymes like Alkaline Phosphatase (ALP), Aspartate aminotransferase (AST) and Alanine aminotransferase (ALT) of protein– carbohydrate metabolism were observed in the three consecutive years, viz 2008-2010 at 24h, 48h and 72h. Results of activity of enzyme like ALP, AST and ALT were examined in the three important tissues like muscles, liver and gills. Year wise study revealed that in year 2010 non-treated fish showed very high enzymes activity which was clearly showed the pollution burden inthe lake followed with temperature variation. It reflects that toxicity factor is temperature, time and dose dependent phenomena. Enzymes activity of treated fish showed overall increase in activity of carbohydrate metabolism which may be due the denaturing of site of interaction or to overcome the stress. This may be related to the morphology and physiology of fish which certainly associated with structural damage. The interruption of biochemical and physiological integrity is computable by the changes in the enzyme activities in liver, muscles and gills. Transamination is one of the fundamental pathways for the biosynthesis and deamination of amino acids, allowing carbohydrate and protein metabolism during variable energy demands of the fish under different adaptive situations. Elevated transaminase levels showed liver damage/ hepatitis, related liver morphology and physiology affected by fluoride results in the failure of liver function. Alteration in enzymes activity was significantly highlighted on carbohydrate metabolism in gills, liver and muscles where overall increase in concentration of carbohydrate from 2008-2010 was observed. A slight variation in 2008 at both applied dose of fluoride (p < 05) while non-significant variation in protein in three important tissues in 2008 reflects less pollution burden while investigation of 2010 showed sharp decline in proteins contents of fish. It was revealed that the lipid was the major source of energy under stress in the three year period of study due to non-utilization of carbohydrate or inhibition of oxidation of carbohydrate to produce energy. In control fish lipids content were higher in three years. They may be the provider of energy for survival under fluoride contamination. Decline in lipid content during three years of investigation support the above hypothesis. It was observed that sub lethal physiological effects of fluoride on macro and micro metals residue accumulation in functional organ showed high concentration of essential(Na, K, Ca, Mg) and non-essential metals(Pb,Hg,Co,Cd). This may be due to fluoride induced permeability in gills, liver and muscles tissues which results in mineral nutrients unbalancing owing to free movement of non-essential metals (Pb, Hg, Co and Cd) in organs of fish under studied. Higher concentration of toxic metal in fish may be related with the altered enzymes and protein glucose metabolism which in turn related with permeability of gills and liver epithelium and dissolution of muscles tissues, which significantly affects the scale loss due to fluoride mobility with increase in metalaccumulation in tissues of fish. Fluoride caused serious pathological liver conditions including shrinkage of liver cells characterized by the dissolution of the liver, blood clots, necrosis and other degenerative changes. Heavy metals may change the cell membrane permeability and due to inactive or denatured enzymes cause dysenzymia. Inhibition of both transaminase suggested that fluoride affect the intermediary metabolism which in turn decrease the production of energy in term of ATP through TCA cycle. The measurement of enzymes ALT, AST and ALP in muscles indicate metabolic disorders including diabetes mellitus, renal failure etc might be related to increase in glucose concentration. While decrease in protein concentration may be related to conversion of protein to energy production via gluconeogenesis to overcome the stress for fish survival. The decrease in glucose level in muscles may be also related to perturb carbohydrate metabolism which was insufficient for energy demand of fish for survival in stress. It was suggested that higher electronegativity of fluoride play a crucial rule in oxidation and degradation of tissues and also reaction of fluoride with oxygen suppresses the oxygen absorption by which energy demand of fish cannot meet by oxidation of carbohydrate therefore concentration of carbohydrate increase with time due to non-utilization in energy production. The depletion in protein content of muscles by fluoride due to inhibition of amino acids metabolism, preventing cells from synthesizing protein or depletion may be of its utilization in energy production. The decrease in protein in muscles may be due degradation and possible utilization for metabolic purposes. The decrease in total lipids may be due to inhibition of lipids synthesis by fluoride as well as increase utilization of stored lipids as a source of energy to conduct regular metabolic function." xml:lang="en_US