Studies were conducted using four elite rootstock scion combinations of arabica coffee and respective pure line scion materials to understand drought tolerance ability by studying the changes in biochemical, chlorophyll fractions and photosynthetic parameters at different soil moisture regimes. The results indicated significant (p < 0.05) reduction in relative water content, nitrate reductase activity, carbohydrate and starch content besides increase in epicuticular wax, free proline, protein content at water stress conditions in rootstock scion combinations and counterpart pure line scion seedlings. At water stress conditions Sln.10 scion on Sln.11 rootstock and S.795 and S.4202 scions on Sln.9 rootstock maintained significantly (p < 0.05) higher relative water content, net photosynthesis, carboxylation efficiency, instantaneous water use efficiency, nitrate reductase enzyme activity, mesophyll efficiency along with high accumulation of epicuticular wax, free proline, total protein and Chlorophyll `b’ content. Maintenance of higher carbohydrate and starch content and recovery to normalcy after the alleviation of stress was observed in these rootstock scion combinations compared to pure line scion seedlings and other combinations indicating better drought endurance ability of these combinations. These combinations could be assessed in the field for yield components and further for commercial exploitation.