Water‐gated organic field‐effect transistors (WGOFETs) are relevant devices for use in the fields of biosensors and biosystems. However, real applications require very stringent performance in terms of electrochemical stability and charge mobility to the organic semiconductor in contact with an aqueous environment. Here, a comparative study of two small‐molecule electron‐transporting perylenediimide semiconductors, which differ only in the N‐substituents named PDIF‐CN2 and PDI8‐CN2 is reported. The two materials present similar solid‐state arrangements but, while the PDI8‐CN2 shows a more 3D growth modality and electron mobility independent of the semiconductor layer thickness (≈10−4 cm2 V−1 s−1), the PDIF‐CN2 has an almost‐2D growth modality and the mobility increases with the semiconductor film thickness, reaching a maximum value of ≈5 × 10−3 cm2 V−1 s−1 at 30 nm. Above this …