This study aimed to identify the maturity-related differences and its influence on the physical fitness, morphological and performance characteristics of young elite paddlers. In total, 89 kayakers and 82 canoeists, aged 13.69 ± 0.57 years (mean ± s), were allocated in three groups depending on their age relative to the age at peak height velocity (pre-APHV, circum-APHV and post-APHV) and discipline (kayak and canoe). Nine anthropometric variables, a battery of four physical fitness tests (overhead medicine ball throw, countermovement jump, sit-and-reach test and 20 m multistage shuttle run test) and three specific performance tests (1000, 500 and 200 m) were assessed. Both disciplines presented significant maturity-based differences in all anthropometric parameters (except for fat and muscle mass percentage), overhead medicine ball throw and all performance times (pre > circum > post; P < 0.05). Negative and significant correlations (P < 0.01) were detected between performance times, chronological age and anthropometry (body mass, height, sitting height and maturity status), overhead medicine ball throw and sit and reach for all distances. These findings confirm the importance of maturity status in sprint kayaking and canoeing since the more mature paddlers were also those who revealed largest body size, physical fitness level and best paddling performance. Additionally, the most important variables predicting performance times in kayaking and canoeing were maturity status and chronological age, respectively.