The changes in phytoperiphyton growth using algal density and ash free dry weight (AFDW) for 28 days colonization time in a brackish water pond during wet and dry seasons were studied. Twenty-four artificial substrata were evenly installed at the bottom of a 1000-m2 pond. Three substrata were removed every sampling for numerical and gravimetrical analyses before and after increasing the pond water at approximate depths of 5, 10, 15, and 30 cm, a practice of growing natural food prior to milkfish (Chanos chanos Forsskal) stocking. Changes in algal density during the wet season varied irregularly and were not related to colonization time; while during the dry season, colonization time affected density with significantly high values from 16th to 28th days. The influence of colonization time on the AFDW was evident for both seasons. During the wet season, significantly higher values were measured from 21st to 28th days of colonization; while during the dry season, significantly high values were measured on the 28th and 21st day to 23rd day of colonization. The phytoperiphyton biomass during the dry season reached 1.2 kg m−2, but only 240 g m−2 during the wet season. There was a linear relationship between density and biomass during the dry season but not during the wet season. Growth rate changed each time water level was raised. Higher growth rate was observed every after addition of water with values ranged from 0.46–0.54 g m−2 and 0.50–0.52 org m−2, and before addition, this decreased to 0.21–0.25 g m−2 and 0.19–0.22 org m−2 for AFDW and algal density, respectively.