Groundwater ecological assessment studies have increasingly gained prominence during the last decade. In order to unravel the overall functioning of these ecosystems, it is urgently necessary to understand the aquifer recharge processes and their influence on the subsurface communities. Arid zone Western Australia calcrete aquifers have been recently found harboring a huge array of biodiversity. As well as their intrinsic ecological value, these environments represent interesting and relative pristine model systems to study several groundwater dynamics. This study embraces three main objectives: 1) recover quantified information about the geochemistry and biology of a calcrete aquifer (Yilgarn Region: Sturt Meadows aquifer), 2) investigate the ecological status of the ecosystem by using macroinvertebrates as biological indicators and 3) assess the influence of rainfall recharge events on the groundwater stygofaunal community. Based on previous investigations, physicochemical (temperature, conductivity, depth, pH, DO and ORP) and biological (α diversity) data from several years (2005, 2006, 2011 and 2015) were available. In order to decipher the recharge effect of the rainfall events on the system, we specifically focused on 2005, the only year with data from 2 different sampling periods (March and September). The physicochemical results revealed a fluctuating tendency over time, mainly due to the unpredictability of the rainfall episodes. Interestingly, 2005 trends were anomalous, with a substantial shift between wet (usually in March) and dry seasons (usually around September). Both geochemical and biological patterns revealed a strict linkage between the aquifer recharge and the ecological switches within the community. In addition, the biological diversity indexes showed specific stygofaunal community responses to the changing environmental conditions. This preliminary investigation informs responses to climate change, especially due to altered rainfall patterns, leading to a broader understanding of the ecosystem functions and the dynamics that regulate the water quality.