In the present study, the biological diatom index (BDI) and the trophic diatom index (TDI) were applied for the assessment of ecological status and water quality of surface and dug wells in Asir region, at the first time of Saudi Arabia. A total of 22 diatom species were identified and used to calculate the diatom indices. The species composition and distribution differed between surface and groundwater sites. Based on BDI and TDI values, the water quality of surface waters (dam reservoirs and streams) ranged between bad and moderate qualities and varied from poor to moderate for dug well water. These diatom indices were significantly correlated with most environmental variables, particularly nitrate and silicate concentrations in these water bodies. Thus, the BDI and TDI are useful metrics for trophic status and water quality assessment in this area and could be adequately applied in other tropical regions for water monitoring purpose.