The wealth of aquatic living resources was assumed to be an unlimited gift of nature. This myth has faded in the light of the realization that aquatic resources, although renewable, are not infinite and need to be properly managed, if their contribution to the nutritional, economic and social well-being of the growing world population is to be sustained. Fisheries operations need to emphasize policy reform, explicit environmental and continuous monitoring for fisher-folk community development. Based on above perspectives this study was aimed to determine the spatial distribution, fisheries diversity, water quality and surrounding environment of some specific rivers, lakes and estuarine areas in Malaysia which have been distressing by human activities since a decade. The fishing gear will be consisted of gill nets, cast nets to catch all sizes of fish. The specimens will be fixed in 10% formalin solution and also preserved in 70% alcohol at the laboratory of the Faculty of Science, International Islamic University of Malaysia Kuantan campus. The morphological characteristics of the collected fishes will be documented by pictorial evidence as well reference for publication. The physico-chemical parameters: temperature, pH, dissolved oxygen, Nitrate, Nitrite, pH, total dissolved solids, total suspended solids and conductivity of both upstream and downstream of the riverine/estuarine water will be measured by using ‘Hydro lab’. Three community indices were utilized to determine fish community structure: species diversity, species evenness and species richness. The Shannon-Weiner diversity index, Berger‐Parker dominance will be applied to measure the species diversity of fish. It is expected that the findings from this study will be helpful to formulate the long term monitoring approach by the relevant authorities for the sustainable development of fisheries resources of these selected water bodies in this tropical environment in Malaysia.