• Disturbance from land use change and tsunamis impact Chilean invertebrates. • Aquatic and terrestrial communities respond differently to wetland disturbance. • Coastal wetland invertebrate communities vary with latitudinal gradients. • Disturbance impacts on size vary according to salinity. • Taxonomic diversity and size-based metrics detect different disturbance impacts. The frequency and intensity of extreme events in coastal wetlands is increasing due to climate change. These, in combination with other threats such as habitat loss, can have strong effects on the biodiversity and ecosystem services of coastal wetland ecosystems. Here we examined how traditional (community composition and taxonomic diversity) and alternative indices based on body size (size diversity and the slope of size spectra) respond to single and combined effects of anthropogenic disturbances, extreme event disturbances, and key environmental drivers, for both aquatic and terrestrial invertebrates in Mediterranean coastal wetlands in Chile. We studied 18 coastal wetlands over more than 500 km along the Chilean coast. We applied both univariate (GLMMs and GAMMs) and multivariate statistics (RDA and variation partitioning) to identify additive and non-additive effects on invertebrates. We also examined latitudinal trends, and tested the potential of alternative metrics to detect interactions between disturbances. We found latitude-specific vulnerability to disturbances in Chilean coastal wetlands. Non-additive effects were more important for aquatic invertebrates, while additive effects were more important for terrestrial invertebrates. In many cases, disturbance effects depended on the environmental conditions of study sites, especially salinity. This study suggests that size-based metrics may be better than taxonomic metrics at detecting interactions among different disturbances, especially for aquatic invertebrates.