This thesis presents a study of the marine habitats of Bahrain together with details of some of the physical factors which may effect the distribution of those habitat types. Satellite remote sensing techniques were employed together with aerial photography and in-field 'ground-truthing' to locate 8 distinct habitat type. A comparison between the satellite-predicted habitat types and the actual habitats present reveals an accuracy of greater than 87%. Over 250 intertidal and subtidal study sites were surveyed for community type, key species, water quality measurements and seasonal variation. A final map of 12 habitat types was produced by expanding on the satellite characterisation using results from the detailed field surveys and the aerial reconnaissance. A set of sensitivity maps was drawn up to identify areas of commercial and scientific importance and to allocate areas in need of conservation, protection and management. The importance of each habitat type and its role in the overall ecosystem is discussed. The findings of this survey constitute the foundations for an effective national marine conservation strategy. Seagrass beds are identified as one of the most important habitat types around Bahrain and the effects of temperature, depth and salinity on the distribution and biomass of the three native species of seagrass are investigated. These three factors are identified as being the most variable physical factors likely to constrain seagrass growth and distribution. 14 sites were surveyed at different seasonal periods to collect data on the biomass, leaf length and leaf number of the different species of seagrass along with temperature, depth and salinity data. The leaf measurements and biomass data from the 3 species of seagrass show a clear relationship to physical factors. Temperature effects the growth of all 3 species to a varying extent. Water depth influences the distribution and growth patterns of Halodule uninervis and Halophila stipulacea. Salinity has no apparent effect on biomass or distribution. The possibility that salinity influences growth pattern and leaf morphology, particularly in Halophila ovalis, is inconclusive and would require further investigation.