Due to their shallow and confined nature, lagoons provide excellent conditions for the transmission of digenean trematode parasites that require two or more intermediate hosts for the completion of their complex life cycles. However, these unstable environments are characterised by an internal heterogeneity and a large variation of a range of abiotic variables. We conducted a series of experiments in a comparative framework to assess the effect of a number of exogenous factors known to exhibit marked fluctuations in the lagoonal environment, i.e. temperature, salinity, water level and photoperiod, on larval emergence of two sympatric parasites, Cainocreadium labracis and Macvicaria obovata, which share the snail intermediate host, Gibbula adansonii, and a sit-and-wait downstream host-finding strategy. Our results demonstrated contrasting patterns and rates of larval emergence indicating an overall differential response of the two species to the variation of the environmental factors. Cercariae of M. obovata exhibited increased emergence rates at elevated temperature (with a sharp increase at 15 °C), decreased salinity (35-25 practical salinity units (psu)) and low water levels, whereas larval emergence of C. labracis was unaffected by the experimental variation in temperature and water level and showed decreased rates at decreased salinity levels (35-25 psu). The differential impact of the variable environmental conditions indicates the complexity of the patterns of exogenous control modifying parasite transmission and abundance in the lagoonal environment. Most importantly, the contrasting rhythms of larval emergence indicate endogenous control associated with the different transmission pathways of the two opecoelid digeneans.