Stumpy irrigation water availability is extremely important for sugarcane production in Pakistan today. This issue is rising inversely to river flow due to inadequate water distribution and an uneven rainfall pattern. Sugarcane growth faces a shortage of available water for plant uptake due to the low water–holding capacity of sandy loam soil, particularly under conventional flood irrigation methods. To address this problem, sugarcane clones were evaluated for their agronomic and physiological traits under conditions of low water availability in sandy loam soil. Ten cane genotypes, HSF–240, SPF–213, CPF–249, CP 77–400, S2008–FD–19, S2006–US–469, S2007–AUS–384, S2003–US–633, S2003–US–127, and S2006–US–658, were exposed to four levels of water deficit created through skip irrigations. These deficit levels occurred during the 9th, 11th, 13th, and 16th irrigations at alternate deficit levels between 2020 and 2022. Physiological data were collected during the tillering and grand growth stages (elongation) in response to the water deficit. The sugarcane clones S2006–US–658, S2007–AUS–384, and HSF–240 exhibited resistance to low water availability at both the tillering and grand growth stages. Following them, genotypes S2006–US–658, S2007–AUS–384, and HSF–240 performed better and were also found to be statistically significant. Clones susceptible to water deficit in terms of growth and development were identified as CP 77–400, S2008–FD–19, S2006–US–469, and S2003–US–633. These genotypes showed reduced photosynthetic rate, transpiration rate, stomatal conductance, relative water content, cane yield, and proline content under stressed conditions. Therefore, genotypes S2006–US–658, S2007–AUS–384, and HSF–240 were better performers concerning physiological traits under water deficit and sandy loam soil in both years. Moreover, a significant positive correlation was assessed between agronomic traits and photosynthetic rats. This study highlights that sugarcane can sustain its growth and development even with less irrigation frequency or moisture availability, albeit with certain specific variations.