Hilsa shad Tenualosa ilisha comprises the largest and most valuable single fishery of Bangladesh. This study was conducted to identify suitable habitats for Hilsa juvenile in the northern Bay of Bengal along the coast of Bangladesh using Geographical Information Systems (GIS) based Multi-Criteria Evaluation (MCE) of water temperature, dissolved oxygen, pH, salinity, turbidity, current, depth and rainfall. Landsat imagery and 8 thematic layers were analyzed with ENVI and GIS capabilities, and developed as a series of GIS models to identify and prioritize the appropriate habitats for Hilsa juvenile. The study covered 29.484 km2 water body and revealed that 56% (16.388 km2) is the most suitable, 21% (6.054 km2) is moderately suitable and 24% (7.042 km2) is not suitable which was consistent with field verification. The assemblage of marinebrackish-freshwater ecosystems with favourable ecological parameters and rainfall patterns are very much important for supporting juvenile Hilsa in the study area. The results are useful for habitat-specific sanctuary development as the efficient conservation may lead to higher production of adult Hilsa and increase the economic benefit to the fishers.