Environmental conditions can easily modulate the abundance of short-lived species, including those of commercial interest. These effects can occur during key periods of their life cycle, such as the spawning and recruitment periods, which are crucial for the stability of natural populations. This study attempts to elucidate the effects of abiotic factors on an important commercial species for artisanal fisheries in the northern Alboran Sea, Chamelea gallina, using CPUE data covering a 16-year period (2004–2020). Generalised Additive Models (GAM) were used to study how the abundance of the species was influenced by a set of environmental variables (sea surface temperature, sea surface salinity, phytoplankton, dissolved oxygen, North Atlantic Oscillation index and pluviometry) at spatial and temporal scale, as well as the spatio-temporal variation considering two areas (eastern and western areas) with different oceanographic conditions. The analysis showed that the abundance of C. gallina showed fluctuations over the historical time series in this ecoregion. The largest catches are observed in the western sector of the northern Alboran Sea, where the local sediment characteristics are more suitable for the species occurrence and the upwelling effect is more pronounced. Results showed that the most influential variables in the abundances during the spawning period were sea temperature, salinity and dissolved oxygen while during the recruitment period were only salinity and dissolved oxygen. Studies on the effects of environmental variables on the life cycle of species are essential to understand complex biological processes such as the spawning and recruitment, especially in commercially exploited species and in highly dynamic environments as the Alboran Sea.