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The City has a total of 115,610 hectares of watershed areas of which five watersheds have major river basins and six have medium-sized river basins.

The five river basins with the largest area include Babuyan River (25% of the total catchment area)Montible River (20%), Langogan River (14%), Inagawan River (12%) and Bacungan River (10%). Irawan watershed, which is the main source of water supply in the City, has a small catchment area comprising only 3% of the total catchment area.

Development of groundwater in the City proper to supply part of its water requirements has limited potential because of low yield and partly salt-water intrusion into the fresh water aquifers. However, groundwater abstraction has a better potential in Sta. Monica, Irawan and Iwahig.

The groundwater quality of the City is relatively poor with a pH higher than 7.2, which is the benchmark for good quality groundwater. The groundwater also has high content level of calcium and magnesium making it hard and produces crust deposits when used in boilers.