The COVID-19 pandemic has emphasized the need for infection risk analysis and assessment of ventilation systems in indoor environments based on air quality criteria. In this context, simulations and direct measurements of CO2 concentrations as a proxy for exhaled air can help to shed light on potential aerosol pathways. While the former typically lack accurate boundary conditions as well as spatially and temporally resolved validation data, currently existing measurement systems often probe rooms in non-ideal, single locations. Addressing both of these issues, a large and flexible wireless array of 50 embedded sensor units is presented that provides indoor climate metrics with configurable spatial and temporal resolutions at a sensor response time of 20 s. Augmented by an anchorless self-localization capability, three-dimensional air quality maps are reconstructed up to a mean 3D Euclidean error of 0.21 m. Driven by resolution, ease of use, and fault tolerance requirements, the system has proven itself in day-to-day use at ETH Zurich, where topologically differing auditoria (at-grade, sloped) were investigated under real occupancy conditions. The corresponding results indicate significant spatial and temporal variations in the indoor climate rendering large sensor arrays essential for accurate room assessments. Even in well-ventilated auditoria, cleanout time constants exceeded 30 min.