Waterflooding is one of the most common secondary recovery methods in the oil and gas industry. Globally, this process sometimes suffers a technical failure and inefficiency. Therefore, a better understanding of geology, reservoir characteristics, rock typing and discrimination, hydraulic flow units, and production data is essential to analyze reasons and mechanisms of water injection failure in the injection wells. Water injection failure was reported in the Middle Miocene Hammam Faraun reservoir at El Morgan oil field in the Gulf of Suez, where two wells have been selected as injector’s wells. In the first well (A1), the efficiency of injection was not good, whereas in the other analog A2 well good efficiency was assigned. Therefore, it is required to assess the injection loss in the low efficiency well, where all aspects of the geological, reservoir and production data of the studied wells were integrated to get a complete vision for the reasons of injection failure. The available data include core analysis data (vertical and horizontal permeabilities, helium porosity, bulk density, and water and oil saturations), petrographical studies injection and reservoir water chemistry, reservoir geology, production, and injection history. The quality of the data was examined and a set of reliable X–Y plots between the available data were introduced and the reservoir quality in both wells was estimated using reservoir quality index, normalized porosity index, and flow zone indicator. Integration and processing of the core and reservoir engineering data indicate that heterogeneity of the studied sequence was the main reason for the waterflooding inefficiency at the El Morgan A1 well. The best reservoir quality was assigned to the topmost part of the reservoir, which caused disturbance of the flow regime of reservoir fluids. Therefore, it is clearly indicated that rock typing and inadequate injection perforation strategy that has not been aligned with accurate hydraulic flow units are the key control parameters in the waterflooding efficiency.