Geosynthetics polymeric materials are recently widely used for geotechnical problems of canals specifically seepage losses with cost-effectiveness, low environmental impact, and quantifiable performance. While the geotextile is one of the geosynthetics, incomat filled concrete mattress is the standard and most famous polyethylene (PE) and polyamide (PA) double woven type of geotextiles. Its main functions are as a liner and/or controlling erosion of soil that creates changes of permeability which could affect the stability of the side slopes of canals. Among irrigation canals in Egypt, Ismailia canal (129.5 km length) is considered the worst case of seepage problems and erosions. The Ministry of Water Resources and Irrigation (MWRI) implemented preliminary technical studies to locate the most critical sections along the canal which seepage losses are the maximum. Lining samples (100 m2, area) by standard incomat were executed in 2016 where four sections of lining with a total length of 61 km were defined. This research assesses the effect of applying the geotextile liner on the slope instability of Ismailia canal at the different proposed four locations of lining where the canal geometry and soil properties are variables. SLOPE/W module of GeoStudio finite element software was used to model the simulation after a clear definition of the soil and geotextile physical properties. The factor of safety, Fs of slope stability for the normal condition of the canal (without lining) ranges from 1.68 to 2.23. The lowest Fs (1.421) was obtained for the first part (km 17.5–28.0) of the second lining section of the canal (km 17.5–38.0) where bed width equals 49 m, maximum and minimum water depth equals 5.79 m and 5.05 m where the soil type is fine sand and the side slopes are 2:1. After implementing the lining, the minimum factor of safety was 1.421 for the same previous location with a 15.57% reduction. The maximum reduction in Fs was obtained for the second part (km 75.0–92.5) of the fourth lining section (km 72.0–92.5) while it records 21.61% with a factor of safety 1.491. Those two parts are critically affected after implementing the lining. However, the maximum reduction in Fs was not exceeded 5% for all sections with sandy clay soil where the Fs did not fall below 1.70. While the geotextile is significant in seepage controlling, particularly at locations where the soil type is coarse sand, specifications and requirements of the thickness uniformity of the mattresses should be achieved for the concrete filling process during the construction and measurements of long-term durability could be considered to sustainably function.