The Putrajaya Administrative area covers 70% of the Putrajaya Lake catchment area. Development work carried out within the Putrajaya area abides by the rules and regulations set by the Putrajaya Corporation to ensure that the quality of the lake water and wetland within the Putrajaya area meets the stipulated benchmark standards. However, 30% of the Putrajaya lake and wetland catchment area is located outside of administration and prerogative of the Putrajaya Corporation. The North Putrajaya catchment area which originates from the Sg. Chuau River contributes the bulk of the water that flows into the lake and wetlands of Putrajaya. Water quality data collected by the Putrajaya Corporation for the period of 2002 to 2005 has been analysed to identify major issues in the Putrajaya Wetland North Catchment area. Data from 2002 shows average percentage parameter of non-compliance 'Putrajaya Standard' for ammoniacal nitrogen (NH(3)-N) at 43.7%, E. coli at 31.3% and TSS at 12.5% while the DO and COD are both 6.2%. For 2003, the average percentage parameter of non compliance for NH3-N was at 23.7%, E. coli at 18.4%, total conform at 18.4%, TSS at 2.6%, DO at 13.2%, COD at 13.2% and BOD at 10.5%. For 2004, the average percentage parameter of non complying for NH(3)-N was at 35.5%, E. coli at 22.6%, total conform at 12.9%, TSS at 9.7%, COD at 3.2% and BOD at 16.1%. For 2005, the average percentage parameter of non compliance were at is 36.4% for E. coli, 22.7% for NH(3)-N, 18.2% for total conform, 13.6% for BOD and 4.5% for both DO and COD. In conclusion the analysed data within the four year period showed that the NH(3)-N and E. coli discharge from the north catchment area did not comply with the 'Putrajaya Standard'. The main factors of water quality issues in the Putrajaya Wetland North Catchment area include the failure of integrating the management of the catchment areas and the stakeholders' attitude of total disregard of the management and control of surface runoff open areas and siltation issues while carrying out development work.