Integrated ecosystem approach is essential to offset adverse impact of transportation network on aquatic habitats in the fragile ecosystem of the Himalayan mountains. It is a cause of concern that the poorly designed network of roads and trails in mountain areas are expanding, without giving due consideration to natural processes of ecosystem function and climatic severity in the Himalayas. These effects have been quantified for a period of three-year (January 2003-December 2005) for hyporheic biodiversity (microphytobenthos, microzoobenthos and macro¬zoobenthos) inhabiting upper Ganges, India (Latitude 290 61/-300 28/ N; Longitude 770 49/-800 6/ E). Transportation network of 495 km long passing along the upper Ganges, a project of US$ 250 million, is one of the most important networks in the mountain region of Garhwal Himalaya. Hyporheic organisms are instrumental for self purification of in¬filtrated water through filtration, sedimentation, deposition and biological decomposition. Hyporheic biodiversity is less known or not at all known in Africa, Latin America, Australia and East Asia. Construction of roads and their widening along the upper Ganges, through massive cutting of mountain slopes, and disposal of tons of the cut material downhill into the waterways has resulted in intensive accumulation of soil, woody debris into the aquatic ecosystem from accel¬erated erosion, gulling and landslides resulting in drastic changes in the physico-chemical and biological profile of the hyporheic biotope. Detrimental effects on conductivity, bottom substrate composition, dissolved oxygen and hyporheic organisms of upper Ganges have been documented. Subsequent to construction and widening activities of roads along the upper Ganges, a decline of 61% in annual mean density, 45% in alpha diversity and 21% in Shannon Wiener index (H) of hyporheic microphytobenthos was recorded during a three-year period. Hyporheic microphytobenthos of upper Ganges were represented by thirteen genera (Diatoma, Navicula, Nitzchia, Pinnularia, Synedra, Acnanthes, Amphora, Coconeis, Cymbella, Fragilaria, Gomphonema, Gryosigma and Hantzchia) of Bacillariophyceae, seven genera (Hydrodictyon, Microspora, Pootococcus, Tetraspora, Spirogyra, Ulothrix and Cladophora) of Chlorophyceae, five genera (Anabena, Nostoc, Oscillatoria, Polycystis and Rivularia) of Myxophyceae and four genera (Gonatozygon, Closterium, Cosmarium, Desmidium) of Desmidiaceae. A decline of 18% in mean annual density, 6% in alpha diversity and 7% in Shannon Wiener index (H) of hyporheic microzoobenthos was estimated. Hyporheic microzoobenthos were represented by seven genera of Rotifera (Ascomorpha, Asplanchna, Brachionus, Lecane, Philodina, Trichocera and Rotaria), nine genera of Copepoda (Diaptomus, Epischura, Cyclops, Mesocyclops, Microcyclops, Achnanthocyclops, Phyllognathopus, Bryocamptus and Parastenocanis) and one genera each of Cladocera (Ceriodaphnia), Ostracoda (Cypridopsis) and Malacostraca (Stygobromus). A depletion of 43% in annual mean density, 38% in alpha diversity and 9% in Shannon Wiener index (H) of macrozoobenthos was computed. Hyporheic macrozoobenthos of upper Ganges were represented by seven genera (Ecdyonurus, Rhithrogena, Ephemerella, Caenis, Baetis, Heptagenia and Cloeon) of Ephemeroptera, nine genera (Hydropsyche, Psychomyia, Polycentropus, Leptocella, Glossoma, Hydroptila, Rhyacophila, Limniphilius, Mystacides) of Trichoptera, eleven genera (Chryogaster, Philorus, Tendipes, Limnophora, Forcipomyia, Pentaneura, Tabanus, Simulium, Dixa, Atherix, Antocha) of Diptera, three genera (Psephanus, Heterlimnius, Dinutes) of Coleoptera, four genera (Architestes, Octagomphus, Epicordula and Symptrum) of Odonata and two genera (Perla and Isoperla) of Plecoptera. Most of the members of hyporheic organisms, sensitive to dis¬turbance were completely missing at the impacted sites. The environmental degradation of hyporheic zone, decline in quantity and missing of sensitive hyporheic organisms are believed to have been caused by increased in water temperature, turbidity, total dissolved solids and biological oxygen demand, accompanied by a decline in dissolved oxygen, accumulation of fine silt and suspended solids blocking interstitial spaces in the hyporheic zone. We have recommended the following mitigation measures to restore habitat quality and protection of hyporheic organisms: ‘functional habitat’ recovery by physical reconstruction of channels based on geomorphological principles, removal of obstructions (gravel mining, and dredging in the impacted site), protecting of riparian vegetation, natural recovery of watersheds, sustainable approaches to road construction and widening, proper drainage of water saturated mountain slopes and spring runoff during heavy precipitation, sealing of side drains against water penetration into the under¬ground alongside fragile sections of the highway, construction of check dams for protection of steep gullies and side erosion of the river bed for maintaining rich heterogeneity of river bed habitats, following minimum flow principle in the river and the establishment of strong co-ordination among transport planners, geologists, civil engineers, structural engineers, environmental biologists.