Fish dwelling in remote mountain water systems are sensitive to long term exposure of POPs and can be used as an important bioindicator of POPs pollution in fragile mountain ecosystems. Current study aimed to investigate the concentrations and patterns of organic pollutants in fish tissues from different lakes of the Lesser Himalayan Region (LHR). OCPs, PCBs, PBDEs were analyzed in four common edible fish species of the LHR: Oncorhynchus mykiss, Labeo rohita, Hypophthalmichthys molitrix and Orechromis aureus. The fish were collected from lakes with different types of catchment areas (glacial, non-glacial mountain region and urban region) and extent of anthropogenic influence. The levels OCPs, PCBs and PBDEs analyzed in the selected fish species were in range of 0.21-587, 6.4-138 and 1.2-14 ng g(-1) lw, respectively. The SDDTs, higher chlorinated PCBs, tetra- and pentaBDEs were more prevalent in urban and remote lakes whereas pp'-DDE, lower chlorinated PCBs and BDE-47 and -99 were predominant in fish species from glacial lakes. SDDTs, SPCBs and SPBDEs showed statistically significant differences (p < 0.05) among species, trophic guilds (carnivore, herbivore and omnivore) and feeding regimes (surface, bottom and column feeder) and SHCH showed a significant difference only among trophic guilds. The stable isotope values of delta N-15 and delta C-13 differed significantly among species for SSHCH, SPCBs, SPBDEs (p < 0.05) and SDDT (p < 0.01). The range of delta C-13 values (-34 to-19%) indicated the importance of littoral and pelagic sources of dietary carbon. Trophic position and dietary proxieswere identified as important variables for explaining the variability of the studied compounds. Kohonen self-organizing maps (SOM) showed that in addition to trophic position and other physiological characteristics of fish, that the type of lakes and proximal sources of POPswere the most important predictors for distribution of organic contaminants in fish samples from LHR.