Résumé: Planktonic ciliates constitute a fundamental component among microzooplankton and play a prominent role in carbon transport at the base of marine food webs. How these organisms respond to shifting environmental regimes is unclear and constitutes a current challenge under global ocean changes. Here we examine a multi-annual field survey covering 25 years in the Bahfa Blanca Estuary (Argentina), a shallow, flood-plain system dominated by wind and tidal energy. We found that the estuary experienced marked changes in wind dominant regimes and an increase in water turbidity driven from the joint effect of persistent long-fetch winds and the indirect effect of the Southern Annular Mode. Along with these changes, we found that zooplankton components, i.e. ciliates and the dominant estuarine copepod Acartia tonsa, showed a negative trend during the period 1986-2011. We showed that the combined effects of wind and turbidity with other environmental variables (chlorophyll, salinity and nutrients) consistently explained the variability of observed shifts. Tintinnids were more vulnerable to wind patterns and turbidity while showed a loss of synchrony with primary productivity. Water turbidity produced a dome-like pattern on tintinnids, oligotrichs and A. tonsa, implying that the highest abundance of organisms occurred under moderate values (similar to 50 NTU) of turbidity. In contrast, the response to wind patterns was not generalizable probably owing to species-specific traits. Observed trends denote that wind induced processes in shallow ecosystems with internal sources of suspended sediments, are essential on ciliate dynamics and that such effects can propagate trough the interannual variability of copepods.