Accurate detection of sub-millimeter defects in reactor core-plate cotter-pin holes is essential for nuclear safety. However, underwater inspection images often suffer from low signal-to-noise ratios, weak boundary responses, and pseudo-edge interference, resulting in unstable localization of defects. Existing deformable and attention-based detectors remain vulnerable to sampling drift and semantic–boundary inconsistency under such conditions. To address these challenges, an Edge-Geometry-Guided Deformable Detection Network (EGD-Net) is proposed for underwater defect detection. EGD-Net introduces an edge-geometry-constrained deformable sampling mechanism that embeds edge-confidence priors into deformable convolution to improve boundary-aware feature sampling. A cross-level semantic–geometric alignment strategy is designed to enhance the interaction between defect semantics and geometric boundary cues, while a top-down feedback recalibration mechanism improves multi-scale response consistency for weak defects. Experiments on the Core-Plate Pin-Hole Defect (CPHD) dataset demonstrate that EGD-Net achieves the highest AP@[0.5:0.95] on both datasets while maintaining competitive or superior Precision, Recall, and F1-score while reducing engineering center error under a fixed operating point. Performance across the two complementary domains suggests its robustness to variations between coupon images and practical underwater inspection scenes. These results indicate that EGD-Net provides a reliable solution for boundary-sensitive localization of underwater sub-millimeter defects in nuclear inspection.