The impacts of climate change on the structure and functioning of estuaries is a major focus of concern, even more when the affected species support important fisheries as the bivalves Ruditapes decussatus, Ruditapes philippinarum, Venerupis corrugata, and Cerastoderma edule in Europe. Their reproductive performance, in the context of climate stressors, had not been investigated so far. Our objective was to experimentally evaluate acute stress effects over gonad development after 6 days of low salinity stress in autumn, winter and spring as well as 4 days of heatwave stress during emersion in summer. These are the most probable extreme events that bivalves should face in our latitudes. Four different salinity ramps (5–20, 10–25, 15–30, 30–30) were created during simulated tidal cycles in mesocosms for the low salinity experiments. Also four sediment heatwaves at emersion (20–20, 20–27, 20–32, 20–37°C) were done during simulated tidal cycle. Both low salinity and heatwave stresses over such short periods compromised reproduction; the acute response was species-specific and varied with the time of the year, and therefore, with the stage of the gametogenic cycle. In December, during sexual resting and the beginning of gametogenesis, a delay in gametogenesis at lower salinities was recorded in the four species. However, at the peak of the reproductive period (March and May), different responses were observed: abnormal oocytes in R. decussatus and resorption of gametes with haemocytic infiltration in R. philippinarum and V. corrugata. Likewise sediment temperatures higher than 32°C provoked gonadal resorption and severe haemocytic invasion in V. corrugata, R. decussatus, and C. edule but had no effect in R. philippinarum. These responses to both environmental stressors might be related to the allocation of energy from reproduction toward defense and repair mechanisms to ensure survival. Contrastingly, low salinities triggered massive spawning in C. edule that could lead to a mismatch between the presence of larvae and phytoplankton, causing potentially starvation and thus reducing recruitment success. Reproduction of theses bivalves would be compromised if low salinity episodes in winter and spring, even for short periods of time such as those in these experiments, are followed by a heatwave in summer. Furthermore the impact would be magnified if this situation happens during consecutive years preventing replenishment of the shellfish beds.