This study aimed to identify the key technical and training-related factors that differentiated among performance levels in short-course (25 m) 100-m breaststroke swimmers. Sixteen male athletes were divided into two groups: Level 3 (682.3 ± 42.3 FINA points) and Level 4 (574.4 ± 28.7 FINA points). Anthropometry, muscle force characteristics, stroke efficiency, and underwater performance were assessed under competition conditions. A Bayesian regression model revealed that Level 3 swimmers achieved significantly faster 100-m times than Level 4 swimmers (β = 1.16, SE = 0.36, 95% CI [0.43, 1.87]). No significant between-group differences were observed in maximum voluntary force (Fmax), the rate of force development (RFD), or basic anthropometric variables, suggesting that strength and body size alone did not explain performance disparities. In contrast, Level-3 swimmers demonstrated a superior stroke index in the first half of the race, as well as significantly greater start-dive velocity and turn-dive length. Bayesian regression confirmed a decisive interaction between turn-dive length and start-dive velocity (β = −0.41, SE = 0.09, 95% CI [−0.59, −0.23]), underscoring the importance of efficient underwater transitions. These findings suggest that beyond a certain threshold, additional strength may not translate into faster race times, whereas technical skill, neuromuscular coordination, and efficient glide mechanics are decisive in short-course performance. Future studies should integrate fat-free mass and drag coefficient measures for a more comprehensive profile of performance determinants, and examine whether the dominance of underwater phases persists in long-course (50 m) pools, where stroke efficiency and in-swim propulsion may play a greater role.