All pollution control activities ultimately aim at maintenance and restoration of the quality of the natural resources. Hence knowledge of the ambient quality of resources is a prerequisite for planning and execution of pollution control management strategies. The Board maintains a network for monitoring of the ambient quality of the rich and varied water resources of the state. There are 3 major schemes for ambient water quality monitoring with the Board. They are
MINARS Programme : Under Monitoring of Indian National Aquatic Resources programme financed by the Central Pollution Control Board this Board has already intensified its activities for monitoring and analyzing the surface water quality of certain selected rivers in the State. In this programme, a total no of 10 (ten) monitoring stations in the Brahmaputra River and its tributaries and 1 (one) in the Barak river have been monitored by the Board regularly at monthly intervals since the year 1987. The programme is still continuing with increasing number of monitoring stations from 11 to 29 (twenty nine) from August, 2002 which includes 10 (ten) ground water samples collected from selected parts of Assam.
| Sl. No. | Name of Rivers | Type | Freq. Of Monitoring | Location of Monitoring Points |
| 1 | Brahmaputra River | River | Monthly | i) at Maijan, Dibrugarh |
| 2 | ii) at Balijan | |||
| 3 | iii) at Nimatighat, Jorhat | |||
| 4 | iv) at Pandu, Guwahati | |||
| 5 | v) at Dhenukhana Pahar, Tezpur | |||
| 6 | vi) at Jogighopa, Bongaigaon | |||
| 7 | Jhanji river | River | Quarterly | at Jhanji, Sibsagar. |
| 8 | Dhansiri river | at Golaghat. | ||
| 9 | Subansiri river | at Gerukamukh, Lakhimpur | ||
| 10 | Elenga Beel | Pond | after confluence with HPC effluent at Jagiroad | |
| 11 | Desang river | River | at Gudamghat, Sapekhati | |
| 12 | Buridihing river | at Margherita | ||
| 13 | Borak River | after confluence with HPC effluent at Panchgram, Cachar. | ||
| 14 | Bhogdoi river | at NH crossing, Jorhat. | ||
| 15 | Bharalu river | near Pragjyotish College before confl. with Brahmaputra River at Guwahati | ||
| 16 | Deepar Beel | Pond | at Guwahati. | |
| 17 | Digboi River | River | at Lakhipathar | |
| 18 | Morabharali | River | before confluence with Brahmaputra River at Tezpur | |
| 19 | Joysagar Tank | Pond | at Sibsagar | |
| 20 | Well | Groundwater | Half Yearly | from Doigboi Area, Tinsukia district |
| 21 | Well | Groundwater | from Karbi Anglong | |
| 22 | Well | Groundwater | from Sibsagar | |
| 23 | Well | Groundwater | from Sibsagar | |
| 24 | Well | Groundwater | from Jorhat | |
| 25 | Well | Groundwater | from Silchar | |
| 26 | Well | Groundwater | from Barpeta | |
| 27 | Well | Groundwater | from Bongaigaon | |
| 28 | Well | Groundwater | from Guwahati | |
| 29 | Well | Groundwater | from Guwahati |
The State of Assam is full of small lakes and tanks. The water quality of these lakes and tanks are being monitored time to time.
Also ground water monitoring of certain sensitive areas of the State have been carried out by this Board in time to time and such activities are still in progress whenever it is found necessary. The district wise ground water quality of some selected areas of the districts have also been monitored under the project called Zoning Atlas for Siting of Industries and is still going on.
Also, effluent discharged by all major industries including hazardous ones in the State are monitored in monthly basis whereas other smaller industries are monitored periodically or as and when necessary.