Sampling was done in duplicates during dry (May 2014 and February 2015) and wet season (September 2014 and November 2014) following the blocking scheme for the nutrient trends. As for the nutrient loading, water samples were collected in three ponds after flooding (water intrusion) and prior to draining (water release). Colorimetric analyses by UV-Vis Spectroscopy following the US EPA standard methods were used to determine the samples’ nutrient levels specifically, ammonia, nitrate, nitrite, and phosphorus. Results showed that ammonia had the highest levels followed by phosphorus, nitrate, and nitrite. Geographically, higher concentration of nitrogen and phosphorus were observed in Eastern Bulacan aquaculture farms, which is attributed to the farmers’ disregard of the important pond preparation activities. Varying seasonal trends were noted among nutrient species due to the different reactions of each analyte under changing climatic conditions. Nutrient levels in sediments were several folds higher than that in the water column. Results of correlation analyses of nutrients in water and sediments showed: a) a good correlation for phosphorus, b) weak correlation for ammonia, and c) no correlation for nitrites and nitrates, implying that sediments maybe a possible contributor of phosphorus and ammonia in water but not nitrite and nitrate. Ammonia and TKN were significantly higher during the flooding suggesting that water coming in to the pond already contains high levels of said nutrients possibly due to higher organic load. Conversely, nitrite and nitrate levels were significantly higher during the draining suggesting transformation of ammonia into these less toxic substances by nitrifying bacteria.