Flood is a common natural disaster occurring almost every year in Malaysia and it’s impact seems to have increased in Kuantan in recent years. Some impacts of flood in urban and rural areas are already assessed directly or indirectly. Unfortunately, impacts of flood on abiotic and biotic components of river ecosystems are not assessed yet specially for Kuantan river although Kuantan river plays an important and lifesustaining role for many inhabitants in Kuantan. Therefore, the proposed study is designed to assess the impacts of flood on (i) nitrogenous and phosphorous nutrients, (ii) structure of the micro-communities (bacteria, phytoplankton, zooplankton, benthic micoinvertebrates), and (iii) growth and condition of fish in the Kuantan river. For this study, a total of five samplings will be conducted at the Kuantan river for a period of nine months from 1st April to 31st December 2015. For this study, samples will be collected at three stations: the Kuantan river estuary (mouth), and 5 km and 10 km upstream of the Kuantan river estuary. Pre-flood and post-flood data on nutrients, plankton, benthic microinvertebrates, and growth and condition factor of fish will be analyzed using appropriate statistics to assess the impacts of flood. A multivariate statistical techniques will also be used to elucidate the important factors that affects nutrients, micro-communities, and growth and condition of fishes in the Kuantan river. This study would be useful for policy making to manage the abiotic and biotic components of Kuantan river ecology. The proposed study would also be helpful in designing ecological monitoring programmes in order to understand the river nutrients and community dynamics before and after flood.