This study aimed to augment existing knowledge of the reproductive characteristics of Donax trunculus through analysis of timing variations and the influence of shell size on partial fecundity (PF) during the reproductive period. To achieve this objective, two reproductive timing characteristics were also studied: size at first maturity (SL50) and the reproductive cycle using histology and image analysis techniques. SL50 was 10.83 mm for females and 10.86 for males. Donax trunculus showed a continuous and simultaneous release of gametes and high oocyte regeneration ability during the reproductive period (from February to July). These reproductive characteristics impeded the estimation of total fecundity. However, throughout the reproductive period an increasing pattern of PF was observed followed by a significant drop at the end of the same period, which could be quantified (293,390 of vitellogenic and ripe oocytes). At the same time PF quantifications allowed for predicting and estimating the influence of shell length (SL) on the reproductive output as a function of oocyte typology (PF = 4.12 + 3.96 SL; r2 = 0.86; all types). Levels of prevalence of a digenetic trematode-like parasite with castrate ability fluctuated between 0–20% depending on the time of the year and sex. In addition, the possible consequences of two different scenarios of population size structure on the reproductive output were simulated, and highlighted how beach areas supporting high levels of anthropogenic pressure (Isla Canela) could compromise future recruitments, producing 84% less oocytes than a beach with a lower level of disturbance (Doñana).