The management of water and nutrient ions, such as nitrate, has been studied extensively in recent decades. Increasingly efficient models have been developed for the use of water and nutrients through the automation of fertigation techniques. The application of a fertigation volume for a duration four times longer than applied on the control was evaluated. In Almería (Spain), one pepper crop and two tomato crops—with and without grafting—were grown between Oct. 2013 and June 2014 in a soilless system with a coir substrate. The effects on root growth, plant growth, production, and quality were measured. The following parameters for the fertigation of the nutrient solution and drainage were recorded: % drainage volume, electrical conductivity (EC) of the nutrient solution, pH, and concentration of nitrates and potassium. The absorption of potassium and nitrate, and the nitrate emissions of the drainage were estimated. The results showed an increase in the root volume and an improved distribution in the cultivation unit for the treatment application in the pepper crop. Slowing the applied fertigation improved the absorption of water and nitrates, and the production in the ungrafted tomato and pepper crops, while the grafted tomato crop was unaffected. Nitrate emissions were lower in the evaluated treatment of the pepper and ungrafted tomato crops. The fruit quality parameters were unaffected.