S iwa Oasis, which is included under irrigated lands, considered a part of depressions presents in the western desert. This study aims to show how drainage system, water table level and application of farmyard manure (7 Mg/fed) could influence on some soil physical properties and wheat production for the two years 2014 and 2015 and to evaluate the performance of the existing drainage in Bany Beer. The results showed that, there was a negative significant relationship between drainage execution and organic fertilizer with bulk density besides to the soil salinity, while a positive significant relationship with total porosity, hydraulic conductivity and pore size distribution. Drainage execution led to reduce bulk density by 0.7 % whenever it accompanied by organic fertilizer increased it to reach 1.8 %. So, salinity decreased from 7 and 9 % for the first and second layers while it was 51 and 54 % for the third and fourth layers. Generally, it decreased 21, 14, 52 and 53 % for the 1st, 2nd, 3rd and 4th layers, respectively. Hydraulic conductivity increased 221 % when drainage executed while it was 156 % when drainage accompanied by organic fertilizers applied for improving soil physical properties. There was a highly significant relationship between wheat production and aforementioned treatments when comparing with control. Drainage efficiency increased when spacing between drains was 30 m comparing to 50 m. The yield increased from 18 to 71% for the second year comparing with the first one which increased averagely by 23 to 59%. This might be caused by improving soil chemical and physical properties by decreasing water table level and increasing aeration. So, it is recommended to apply drainage system accompanied by organic fertilizers application in Siwa oasis that suffers from water logging problem.