The lakes are either freshwater or marine, major lakes found in the Kerala are, Vambanad, Ashtamudi, Vellayani Sasthamkotta and Pookot lake. Among the fresh water lakes of Kerala, Pookot lake is the one which has been well studied, The water quality characteristics of Pookot lake is optimum for a productive lake, which is being used for fish culture and recreational purposes The physico-chemical parameters are within the standards recommended for domestic use. Electrical conductivity was found to be in the range 26.7-63.1 micromhos/cm. Total hardness varied between 12 mg/L and 33.3 mg/L. Nitrate and nitrite varies in the range 0.01mg/l-0.5mg/L and 0.001-0.004 mg/L. Seasonal variations of trace metals like aluminum, magnesium, calcium, potassium, sodium, iron and copper showed that their levels are below the permissible limit for potable and agricultural waters (CWRDM Report 1988).

Meteorological, physical and chemical parameters of Vellayani Lake, Kerala, India, have been analysed for twelve months (August 1980 to July 1981), the topography of the lake is described, and correlation coefficients were calculated between meteorological and hydrographical parameters. The results indicate that the lake can be converted into a productive aquafarm by means of slight manuring (Jayachandran and Joseph, 2007). Hydrographical features and prawn fauna of the Veli-Aukulam Lake.  The ranges of various hydrographical features recorded were: Water temperature -27.25 degree (January and July) to 32.10 degree C (April) oxygen content -4.0 (September) to 7.49 mg/l (October); pH - 6.68 (January) to 7.98 (October); Salinity - 0.18 (August) to 4.37% (September); Phosphate phosphorus -2.95 (October) to 8.45 mu g at./l (August); Silicate silicon - 12.2 (September) to 19.65 mu g at./l (February); Nitriate nitrogen - 0.71 (February) to 20.60 mu g at./l (November); Nitrite nitrogen - 0.45 (March) to 5.55 mu g at./l (June). The prawn fauna recorded were Macrobrachium idella idella; M. idae; M. equidens; M. scabriculum; M. veliense (Jayachandran and Joseph, 1985), M. josephi (Jayachandran, 1989); Palaemon concinnus (Dana, 1852); Penaeus indicus (H. Milne Edwards, 1837); Metapenaeus affinis; M. dobsoni.

Prakasam, V.R and Joseph, M.L., (2000) studied the water characteristics of Sasthamcotta Lake, Kerala on the basis of primary productivity. The lake water was clear, soft and acidic. All the physico-chemical characteristics were stable throughout the period of study. The primary productivity of the lake was quite low and it is classified as oligotrophic type. The effects of soap-detergent-fertilizer discharges, as revealed by indicator parameters, were not at dangerous levels. Microbial analysis of fecal coliforms indicated that the water was contaminated with human excreta.

Soman, K and Chattopadhyay, M., (2004) studied catchment characteristics, physical setting including elucidation of geology and geomorphology, landuse, landuse change, water budgeting in GIS environment and water quality the two south Kerala freshwater lakes, namely, Sasthamkotta and Vellayani. Sasthamkotta lake has a projected storage capacity of 30 MCM water at +4 m level, whereas in the case of the Vellayani lake, the maximum possible storage capacity would be just over 5 MCM at a bund height of +1.65 to 1.70 m. Temporal analysis of landuse indicate that changes in landuse pattern in the peripheral areas of the lakes have been enormous over the years. Preservation of adjacent wetlands has been suggested to enhance infiltration into the lakes. Slope protection measures have been suggested to avoid siltation of the lakes, which will be conducive to maintain sustained storage capacity of the lakes.

Devi, et al., 1996, studied the Ashtamudi Estuary. Siltation and decay of organic wastes were the major causes for loss of depth and the decline in transparency values. Lower DO and pH values suggested the extent of pollution contributed by the industrial establishments located on the bank of the estuary. The study highlights the impact of human intervention which has resulted in the deterioration of water quality and the inhibition of various estuarine processes.

Gopakumar., et al., 2007, assess the flood storage capacity of the Vembanad wetland using GIS. Hydrologic analysis indicates that the flooding in the wetland area result from extensive storms covering the associated river basins. Since the water level in the Vembanad Lake is determined by the river flows and tidal conditions downstream, storage effects are also important in the formation of extreme floods in the wetlands. At the same time, the flood storage capacity of the wetland is closely related to the land use pattern.

Water quality status of the rivers of Kerala: The analyses of the Mavattnpuzha river water samples from upstream indicated that the river is very clean with values of pH 6 5-6.7; suspended solid 6-9 4mg/l; BOD within lmg/1, COD 4.1-4,7mg/l; colour 15-19 FT-Co units; chlorides 4.5 - 4.7 mg/1 ; sodium 3,91-4 14aig/l and SAR 0..39-0.52. At the downstream of the effluent discharge point, the increase in the concentration of solids, BQD,COD are reported. BOD is reported to have increased to 4.6-6..3mg/l, CQD to 17-20 mg/1 At the upstream station the coliform count varies from 700-1205 MPN/l00 ml, In the downstream me density of coliform is reported to vary from 517 to 1825 MPN/ 100ml indicating the impact of sewage discharge on the left bank of the river.

In Chlthrapodia river, the concentrations of TDS, Chloide, nitrate, sulphate,  fluoride, calcium and lead were found to be high. Presence of heavy metals such as copper, Zinc, nickel, iron, manganese and chromium were detected in the water samples. The residual analysis of animal and plant tissues showed lead concentration as high as 68 mg/kg and 76.4 mg/kg in fish and prawn tissues respectively ( CWRDM Report 1997).

The water quality of river Bharatapuzha indicated the presence of mineral oil and a high concentration iron (0.69mg/T) in the water samples. Organo chlorine pesticides like hexachlorohexane (14 ng/1) was also detected in the water samples collected.

Maya, et al., (2007) addresses the water quality and nutrient flux of two tropical rivers and discusses the impact of urbanization and industrialization on Periyar and Chalakudy river-water quality. Nutrients in the two rivers reveal marked seasonal and regional concentration variations. The Periyar river shows higher average concentrations of dissolved inorganic nitrogen (DIN) (monsoon 801 g/l and non-monsoon 292 g/l) than Chalakudy river (monsoon 478 g/l and non-monsoon 130 g/l). Dissolved inorganic phosphorus (DIP) has lower average values in the monsoon season (Periyar River, 38 g/l; Chalakudy River, 42 g/l) than dissolved organic phosphorus (DOP) values (Periyar River, 107 g/l; Chalakudy, 62 g/l). The discharge of dissolved silicon (DSi), into the Periyar river (40 193 t/y) is nearly five times higher than that in the Chalakudy river (8275 t y-1). The discharges of dissolved Fe (DFe) through the Periyar and Chalakudy rivers are 257 t/y and 36.7 t/y, respectively.

Sahib, 2004 studied the physicochemical characteristics of the water and phytoplankton in the Kallada River. Out of the 35 species of phytoplankton recorded, Chlorophyceae represented the bulk of the phytoplankton throughout the entire study period. Results indicate decrease in dissolved oxygen and increase in CO2 during rainy season due to the retarded photosynthetic activity of the phytoplankton or to decreased concentration of oxygen being consumed by the organic matter in turbid state of water during low phytoplankton density.

Nair, N.B, et al., 1989, investigations in the Neyyar river, Kerala, India show that riparian vegetation along the stream side in the watersheds from the headwater has much impact on the channel structure such as shading, retention of allochthonous organic matter etc., and the changes in the biological analogue with regard to the organic substance are evident in the stream river network.

 The water quality survey of Punnurpuzha-a river situated near Kozhikode revealed that the water of the river is rather soft and is suitable for all the three major uses-drinking, irrigation, and industry. The total dissolved solid, hardness, and bicarbonate contents of the river water go up during the post-monsoon months (Abbasi, et al., 1996). Water quality of forty two randomly selected open wells along Malappuram Coast (Kozhikode, India) reveal that portability of the majority of the wells (90.6%) is below permissible levels as per the ICMR and WHO standards (Abbasi and Nipaney, 1995).The south central parts of Kerala State exhibit changes in land use from agriculture fields (1974-75) to built-up environment. Flood water transports alluvial sediments and nourishes soil fertility. During summer the acidity of the soil is neutralized by saline water intrusions. Certain recently introduced environmental modifications to control flood water and to regulate salt water entry, with a view to increasing rice production, have largely resulted in deteriorating ecological balance. The consequent results are analysed in the light of irrational water resource management having irrevocable effects on life, life-supporting systems and development of the region. The present status of the above areas calls for greater caution and well planned programs in handling water conservation projects and praticising resource management which have a close bearing on the delicate ecosystems and prevailing environment (Balchand., 1983).

Study was undertaken in the estuarine part of south-western part of Kerala which is bound by three important rivers namely Periyar in the north, Pumba in south and Muvattu puzha in the east, to evaluate the water pollution caused by existing industries in parts of Cochin (Khurshid, 1998). Chemical nature of the surface water bodies from Eloor to Cochin harbour has been made with a view to assess the extent of pollution of various trace elements. The study revealed that the concentration of trace elements around Eloor industrial belt is higher than the Vembanad Lake, which may be attributed to steady discharge of effluents in Eloor region. In most of the samples, concentration of trace elements exceeds the maximum permissible limit prescribed by W.H.O. (1984).

Chalakudy river basin in Kerala was studied (Chattopadhyay, et al., 2005) based on an analysis of 27 water samples spread over five landuse types and monitored during four seasons, substantiated linkages between landuse pattern and water quality. Change in landuse practices, particularly urbanization and intensive agriculture lead to water quality deterioration.. Samples under urban landuse showed poor water quality throughout the year. Correlation analysis of various parameters indicated seasonality in physico-chemical characteristics of river water, which was linked to fluctuations of drainage discharge and changes in landuse pattern.

Unnikrishnan, P and Nair, S. M., (2004) studied the concentrations of dissolved and particulate trace metals (Ni, Pb, Zn and Mn) and their partitioning behaviour between the dissolved and particulate phases in a typical backwater system of Kerala, the southern upstream part of Cochin Estuarine System (South India). They have discussed spatial and temporal variations of trace metals in the dissolved and particulate phases with special reference to pH, dissolved oxygen, salinity and suspended particulate matter. The distribution and partitioning behaviour of trace metals in the water column were found influenced by the presence of a salinity barrier across the backwater system and also by the massive use of pesticides and chemical fertilizers in the vast area of agricultural land near the backwater system. Lack of proper flushing of the backwaters, which receive large amount of trace metals through the application of pesticides and agro-chemicals, due to the presence of the salinity barrier has significantly affected the water quality of the area.

Hydrogeochemistry of groundwater in upland sub-watersheds of Meenachil river, parts of Western Ghats, Kottayam, Kerala, India was used to assess the quality of groundwater for determining its suitability for drinking and agricultural purposes (Vijith, H and Satheesh, R., 2005). The study area is dominated by rocks of Archaean age, and Charnonckite is dominated over other rocks. Rubber plantation dominated over other types of the vegetation in the area. Though the study area receives heavy rainfall, it frequently faces water scarcity as well as water quality problems. Hence, a Geographical Information System (GIS) based assessment of spatiotemporal behaviour of groundwater quality has been carried out in the region. Twenty-eight water samples were collected from different wells and analysed for major chemical constituents both in monsoon and postmonsoon seasons to determine the quality variation. Physical and chemical parameters of groundwater such as pH, dissolved oxygen (DO), total hardness (TH), chloride (Cl), nitrate (NO3) and phosphate (PO4) were determined. A surface map was prepared in the Arc-GIS 8.3 (spatial analyst module) to assess the quality in terms of spatial variation, and it showed that the high and low regions of water quality varied spatially during the study period. The influence of lithology over the quality of groundwater is negligible in this region because majority of the area comes under single lithology, i.e. charnockite, and it was found that the extensive use of fertilizers and pesticides in the rubber, tea and other agricultural practices influenced the groundwater quality of the region. According to the overall assessment of the basin, all the parameters analysed are below the desirable limits of WHO and Indian standards for drinking water. Hence, considering the pH, the groundwater in the study area is not suitable for drinking but can be used for irrigation, industrial and domestic purposes. The spatial analysis of groundwater quality patterns of the study area shows seasonal fluctuations and these spatial patterns of physical and chemical constituents are useful in deciding water use strategies for various purposes.

Rahiman, et al., (2003) examined the bacteriological quality of water from wells at Ponnani, a fishermen dominated coastal region of rural Kerala, India. The quality was assessed in terms of total coliform (TC), faecal coliforms (FC), and faecal streptococci (FS). TC ranged from 0.4 to 110 mL-1, with a mean value of 39.4 mL-1. Mean values of FC and FS were 36.4 and 17.1 mL-1 respectively. FC: FS ratio revealed that most of the samples had human faecal pollution. All the strains of Escherichia coli encountered in the samples showed multiple antibiotic resistance.

5.1 Need for the Study

The rivers of Kerala are monsoon-fed and fast-flowing. According to an estimate (PWD, 1974), the total runoff of the rivers of the state amounts to about 77,900 mm3 , of which 70,200 mm3 is from Kerala catchments and the remaining 7700 mm3 is from Karnataka and Tamil Nadu catchments. The available per capita fresh water resource in Kerala is less than the national average; hence it’s important to conserve the aquatic ecosystems of the state. Aquatic ecosystem conservation and management requires collaborated research involving natural, social, and inter-disciplinary study aimed at understanding various components, such as monitoring of water quality, biodiversity and other activities, as an indispensable tool for formulating long term conservation strategies. In order to get the current status of these threatened ecosystems a state level water quality programme was developed.

Findings of this study address a wide range of water-quality issues related to potential effects on human health and aquatic ecosystems, for example, on

1. The quality of water in streams, public-supply and domestic wells;
2. The role of hydrology and contaminant transport on water quality, drinking water, and ecosystem health;
3. Effects of agriculture and urbanization on aquatic health, nutrient enrichment, and stream ecosystems;
4. Changes in selected contaminants in streams and ground water over time;