The harbour porpoise is the only cetacean species native to German waters. Since human pressures are suggested to shorten their reproductive lifespan, basic knowledge on reproduction is strongly required. One parameter is the onset of sexual maturity in female harbour porpoises. Therefore, we investigated the first signs of sexual maturity for a period of almost two decades (1990–2016). Ovaries from 111 female harbour porpoises from the German North Sea and Baltic Sea were examined for the presence and morphological structure of follicles, corpora lutea and corpora albicantia. Based on the ovarian characteristics we performed the first model-based estimation of age at sexual maturity for harbour porpoises from German waters. Additionally, we produced a demographical age structure based on all female strandings and bycatches from German coasts. Our results showed that corpora lutea and corpora albicantia as signs of former ovulation could be found in individuals at an age of 4.95 (± 0.6) years. No significant differences between specimens from the North Sea and Baltic Sea were detected. However, the average age at death differed significantly with 5.70 (± 0.27) years for North Sea animals and 3.67 (± 0.30) years for those in the Baltic Sea. Growing evidence exists that the shortened lifespan of Baltic Sea harbour porpoises is linked to an anthropogenically influenced environment with rising bycatch mortalities due to local gillnet fisheries. Thus, our findings support the idea of local management plans based on a model-based detection of age at sexual maturity and considering the anthropogenic impacts on the population for effective protection of harbour porpoises and the North Sea and Baltic Sea.