The perspective of climate change and its direct affects on freshwater resources and indirect affects on diversity of fish fauna and freshwater micro-fauna such as zooplankton was presented here. North-eastern India- a mega biodiversity hot spot is considered as a natural resource of observation. Two key environmental parameters such as temperature and rainfall have been investigated in relation to climate change in North-eastern India in general and Tripura in particular. During a period of 28 years from 1982 to 2010 the atmospheric temperature is increased- 17.2-22.12 0C with average increase-0.2 0C per year. Rainfall is decreased from 162 mm to 37 mm, with average decrease- 3.34-5.26 mm per year. Data of CO2 at 0530 hrs shows a mean value- 17.27±6.43 ppm. Hence,data of climate change is relatively greater. Diversity of freshwater fish species in the freshwater ecosystem is reduced to 67 species from 146 species of 1982. Therefore,gradual decrease of rainfall as well as increase of temperature and CO2 over a period of three decades are the results of climate change in freshwater environment of North-Eastern Indian region.