In West Texas, the two major constraints that often limit the cotton production are N fertility and water availability (Knowles et al., 1993; Morrow & Krieg., 1990). Subsurface drip irrigated area under cotton in West Texas is expanding at a rapid rate. Subsurface drip irrigation (SDI) systems are one of the most efficient irrigation systems with efficiency of > 90% (Bordovsky and Lyle, 1998). Though the N fertilizer sources are injected frequently at low rates through SDI, Nitrogen (N) fertilizer use efficiency is not high. Previous studies reported that less than 50% of the N fertilizer injected into a SDI cotton system was recovered in the plant (Chua et al., 2003). Field experiments were conducted to study the effect of source of N fertilizer, the timings of termination of N fertigation and spectral reflectance based application of fertilizer to cotton. The two sources of N fertilizer used were Urea Ammonium Nitrate (UAN) (32-0-0), and Ammonium Thio Sulphate(ATS) (28-0-05), ATS is considered to be a nitrification inhibitor and hence reduce N losses. The timings of termination of N fertigation was mid bloom and peak bloom.