Abstract. Abstract Aim In this study, we investigated the impact of an episodic marine intrusion on the water column characteristics of Jurubatiba lagoon, a tropical coastal ecosystem, for 12 months following a sandbar breaching event to elucidate the duration of its effects. Methods Monthly, we sampled the physical, chemical, and biological characteristics along the water column for one year after a sandbar breaching event and seawater inflow. We assessed the temporal (monthly) and spatial (along depth profiles) associations among these variables and the temporal correlation among vertical heterogeneities in these variables and environmental drivers of stratification. Results Marine intrusion resulted in salt wedges formation in the short-term, leading to stratification in dissolved oxygen, pH, salinity, and chlorophyll-a concentration along the water column for at least four months. However, temperature and solar incidence also emerged as crucial factors associated with vertical heterogeneity in limnological variables, influencing water density and pH throughout the study period. Precipitation and wind speed had only marginal effects on thermal and ectogenic stratifications, probably mediated by water colour, nutrient inputs, water column depth and lagoon’s orientation in the landscape. Conclusions Our data unveiled that, despite their shallowness and wind exposure, coastal lagoons can exhibit considerable vertical heterogeneities in limnological variables due to various climatic and hydrodynamic aspects. Notably, the effects of marine intrusions on salinity and ectogenic column stratification can persist for several months, affecting water quality and, probably, biotic communities and ecosystem functioning. Once human activities and climate change may intensify marine intrusions on coastal lagoons, understanding spatiotemporal dynamics and their drivers is fundamental to anticipating their effects and conserving such vulnerable ecosystems.