Across the globe, Mediterranean regions are shifting to more arid climatic conditions. Changes include increasing temperatures, decreasing rainfall volumes and timing, changing regional wind patterns and increased evaporation rates, all of which affect wetland water regimes. Invertebrates that rely on wetlands risk local extinction unless they have adaptations to withstand prolonged periods of desiccation. Consequently, prolonged drying, and its effects on physicochemical conditions, has the potential to reduce biodiversity at the scale of individual wetlands and at regional scales (through cumulative effects). The aims of this study were to: 1) determine whether climatic drying in the Western Australian Wheatbelt and Great Southern regions affected wetland water regime and water quality in the 13 years between 1998 and 2011; and 2) determine whether the alpha (local), beta (between wetlands) and gamma (regional) diversity of wetland invertebrates changed over the same period Linear regression and multivariate analyses were used to identify temporal changes in wetland inundation patterns, water quality and invertebrate taxa richness, and to identify changes in alpha, beta and gamma diversity of invertebrates from 17 wetlands. Climatic drying was associated with declining depth and increasing frequency of dry periods in wetlands. Gamma and alpha diversity declined across time, but beta diversity (among wetlands) remained consistently high as each wetland retained a distinct fauna. Salinity and average rainfall partially explained invertebrate richness and assemblage composition in wetlands. Wheatbelt and Great Southern region wetlands showed changes in aquatic invertebrate assemblages due to drying water regimes. Western Australia is in an advanced state of climate drying compared to other Mediterranean regions. The results of this study will inform other Mediterranean regions of the biodiversity outcomes of long-term dryness in wetlands with distinct fauna.