Zooplankton assemblages in the confined coastal lagoons of La Pletera salt marshes (Baix Ter wetlands, Girona, Spain) are dominated by two species: one calanoid copepod (Eurytemora velox) and the other rotifer (Brachionus gr. plicatilis). They alternate as the dominant species (more than 80% of total zooplankton biomass), with the former being dominant in winter and the latter in summer. Shifts between these taxa are sudden, and intermediate situations usually do not last more than 1 month. Although seasonal shifts between zooplankton dominant species appear to be related with temperature, other factors such as trophic state or oxygen concentration may also play an important role. Shifts between species dominances may be driven by thresholds in these environmental variables. However, according to the alternative stable states theory, under conditions of stable dominance a certain resistance to change may exist, causing that gradual changes might have little effect until a tipping point is reached, at which the reverse change becomes much more difficult. We investigated which are the possible factors causing seasonal zooplankton shifts. We used high-frequency temperature and oxygen data provided by sensors installed in situ to analyse if shifts in zooplankton composition are determined by a threshold in these variables or, on the other hand, some gradual change between stable states occur. Moreover, following the postulates of the alternative stable states theory, we looked at possible hysteresis to analyse if these seasonal zooplankton shifts behave as critical transitions between two different equilibriums. We also examined if top-down or bottom-up trophic interactions affect these zooplankton shifts. Our results show that shifts between dominant zooplankton species in La Pletera salt marshes are asymmetric. The shift to a Eurytemora situation is mainly driven by a decrease in temperature, with a threshold close to 19 °C of daily average temperature, while the shift to Brachionus does not. Usually, the decrease in water temperature is accompanied by a decrease in oxygen oscillation with values always close to 100% oxygen saturation. Moreover, oxygen and temperature values before the shift to calanoids are different from those before the reverse shift to Brachionus, suggesting hysteresis and some resistance to change when a critical transition is approaching. Top-down and bottom-up forces appear to have no significant effect on shifts, since zooplankton biomass was not negatively correlated with fish biomass and was not positively related with chlorophyll, in overall data or within shifts.