The Pliocene Kafr El-Sheikh (KES) Formation in the onshore Nile Delta region hosts numerous shallow gas accumulations. These are readily detected on seismic profiles by definable direct hydrocarbon indicators (DHI). However, the presence of residual gases causes many production failures. Two shallow (< 1500 m) pay zones were investigated in this study; both display seismic flat bright spots. The shallower pay zone (pay zone 1) comprises prograding distributary channel-fill sandstones, whereas the deeper pay zone 2 constitutes the transgressive distal sand bars. Pay zone 1 sandstones have better reservoir quality in terms of porosity (Av. 25.68%), permeability (86 md), water saturation (Av. 43.26%), and hence host thick gas accumulation (~ 15 m) with high net/gross (N/G) ratio ~ 0.98. On the other hand, pay zone 2 has a significant reservoir heterogeneity and contains only residual gases with N/G ratio of 0.26. The eodiagenetic infiltration of clays (Av. 31.46%), authigenic precipitation of glauconite (Av. 7%), and formation of pseudomatrix materials (Av. 2%) in pay zone 2 sandstones have the most detrimental impact on their reservoir quality. Elevated water saturation in pay zone 2 (Av. 64%) reduced the movable hydrocarbon content and results in accumulation of residual gases. Mild mechanical compaction preserved the intergranular porosity of the pay zone 1 sandstones, and incursion of meteoric water facilitated the dissolution of feldspars, the neoformation of secondary pore spaces (Av. 2.9%), and thus increased the reservoir storage and flow capacities. This study highlights that the initial depositional setting of the shallow siliciclastic reservoirs controls their diagenetic pathways and hence their reservoir quality.