In all global aquatic ecosystems, species composition of micro and macro organisms, abundance, growth, development and their distribution depend on quantity of contaminants, types of contamination; levels of chemical concentrations; sediment load; electrical conductivity; turbidity; seasonal variations; depth, width, flow rate, number of inlets and outlets with volume of water and also the impacts of anthropogenic activities always reflect on the water quality of a wetland. Physico-chemical parameters and planktonic diatoms species composition were studied at five selected sampling stations (C1-C5) along River Kisat from March to August 2016. There are 26 species of planktonic diatoms belong to 13 genus which are Amphora, Aulacoseira, Cyclotella, Cymbella, Diatoma, Fragillaria, Gomphocymbella, Navicula, Nitzschia, Pinnularia, Stephomodiscus Surillela and Synedra. Out of these 26 species, only eight species (Cymbella cistula; Cymbella sp; Diatoma hiemiale; Navicula granatum; Nitzschia lucastris; Nitzschia palea; Nitzchia recta and Nitzschia sub-acicularis) are present in all the five sampling stations, while Fragillaria longissima and Gomphocymbella beccari are present only once in sampling station C4 and C5 respectively. Only genus Nitzschia has five species followed by the genus Aulacoseira represented by three species. There are seven genus which are Amphora, Cyclotella, Cymbella, Diatoma, Fragillaria, Navicula and Synedra represented by two species each, while rest of the four genus including Pinnularia, Gomphocymbella, Surillella and Stephomodiscus are represented only with one species each. The mean monthly values of selected physico-chemical parameters are: electrical conductivity 657.27 ± 186.78 μS/cm, temperature 24.84 ± 0.65°C, pH 7.87 ± 0.24, dissolved oxygen 4.19 ± 0.7 mg/l, turbidity 89.90 ± 9.76 NTU, flow rate 1.38 ± 0.05 km/h; total alkalinity 150.85 ± 28.23 mg/l, total nitrogen 657.27 ± 227.56 μg/l, total phosphorus 677.18 ± 20.87 μg/l, silicates 4.11 ± 0.52 mg/l and chlorophyll-a 130.54 ± 40.15 mg/l. The study revealed that only pH, dissolved oxygen, alkalinity and silicate show significant difference (p ≤ 0.05) along Kisat river but rest of the physico-chemical levels of conductivity, turbidity, total nitrogen, total phosphorus show higher concentrations in river water. It is concluded that the presence or absence of planktonic species and their frequency should be used as bioindicator( s) to assess the status of water quality of any aquatic ecosystem.