A field experiment was conducted to evaluate the agronomic and physiological responses of rice under different water management systems, types of fertilizer and seedling age. This experiment was done at the farm of Agri Park, College of Agriculture, Central Experimental Station (CES), Crop Science Cluster of the University of the Philippines Los Baños, College Laguna during 2013. The strip-split plot design with three replications was used with the two types of fertilizer (vermicompost and chemical fertilizer), water management (with and without standing water) and two seedling ages (10 and 14-d old) were the treatments in the experiment. Chemical fertilizer produced the highest grain yield, total dry matter (TDM), leaf area index (LAI), net assimilation rate (NAR) and crop growth rate (CGR). Most of these characters significantly increased in 10-d old seedlings with chemical fertilizer without standing water. The shorter phyllochron and higher root pulling resistance (RPR) were observed in 10-d old seedlings without standing water. For the variety NSIC Rc 216, the use of 10-d old seedlings grown without standing water with chemical fertilizer is the optimum conditions for the better growth and high productivity.