The wetlands are subjected to a number of environmental stresses and threats which have been in vogue since the last four decades. In addition to natural aging, human encroachments; Conversion of the low lying areas into farms; disposal of untreated domestic garbage, leaching of chemical fertilizers in and around the lake areas; draining of toxic chemicals like DDT, BHC, Aldrin, Endolan, Endosulfan, Rogo etc. for catching fish without much labour are the major causes of degrading and polluting the lakes. The wetland ecosystem is degrading day by day and partially becoming agricultural land due to the impact of soil erosion and urbanization around the lakes.

The Waithou lake was once known to be the breeding place for the threatened fish species Ngaton (Labio bata) till 1971-1972 but after  the construction of the Cheksabi barrage and ringbund during 1970s, the habitat of the fish has been completely vanished from the lake. Other highly degraded lakes in the state are Kharungphat, Khoidumpat, Pumlen, Lokoipat, Sanapat, Yaralpat and Poiroupat.