The impacts of water variation differ in their magnitude in different canal irrigation systems, mainly due to variations in water availability (timings and amounts), crop types and soil fertility status. These necessitates conducting site-specific research and studies to evaluate the impact of variations in water availability at the farm level for specific crops. The findings of such studies will then be utilized to rationalize the irrigation supplies at the farm level keeping in view the level of variation. Accordingly, this study was undertaken for the assessment of inequality in canal water distribution and its impacts on the yield and water productivity of maize in the command area of the Khikhi distributary, Pakistan. For this purpose, three water courses at the head, middle and tail reaches of the distributary were selected. On each of the selected watercourse, three maize fields at the head, middle and tail were chosen. Discharges measurements were taken and the yield of the maize crop was recorded. A significant variation in design and measured discharges were observed in the head reaches (inlet point) of watercourses off taking from the head, middle and tail of distributary that was 13.79%, 12.0% and 7.30% reduction in the flow against the allocated discharges, respectively. The discharge variation along the distributary varies from 0 to 38% from head to tail end, similarly, the variation in discharge for the watercourse located at the head of the distributary was from (100 %) 2.90 cfs to (85.86 %) 2.49 cfs i.e. 0.41 cfs (14.14%) reduction in discharge from head to tail end and for the watercourses located at the middle (WCM) and tail (WCT) the discharge reduction was (31.72%) 1.02 cfs and (37.08 %) 0.66 cfs, respectively. These variations in discharge ultimately reduced the maize crop yield and production from 11 to 54%. The percentage gap in yield from head to tail was up to 54% and the water productivity decreased up to 26% for tail end section of watercourses. These results clearly showed the inconsistency in canal water distribution at tertiary level (watercourse) as well as secondary (distributary) irrigation system leading to reduce the crop production of tail end farmers.