One of the primary indicators of volcanic unrest at Mammoth Mountain is diffuse emission of magmatic CO₂, which can effectively track this unrest if its variability in space and time and relationship to near-surface meteorological and hydrologic phenomena versus those occurring at depth beneath the mountain are understood. In June–October 2013, we conducted accumulation chamber soil CO₂ flux surveys and made half-hourly CO₂ flux measurements with automated eddy covariance and accumulation chamber (auto-chamber) instrumentation at the largest area of diffuse CO₂ degassing on Mammoth Mountain (Horseshoe Lake tree kill; HLTK). Estimated CO₂ emission rates for HLTK based on 20 June, 30 July, and 24–25 October soil CO₂ flux surveys were 165, 172, and 231 t d^{− 1}, respectively. The average (June–October) CO₂ emission rate estimated for this area was 123 t d^{− 1} based on an inversion of 4527 eddy covariance CO₂ flux measurements and corresponding modeled source weight functions. Average daily eddy covariance and auto-chamber CO₂ fluxes consistently declined over the four-month observation time. Wavelet analysis of auto-chamber CO₂ flux and environmental parameter time series was used to evaluate the periodicity of, and local correlation between these variables in time–frequency space. Overall, CO₂ emissions at HLTK were highly dynamic, displaying short-term (hourly to weekly) temporal variability related to meteorological and hydrologic changes, as well as long-term (monthly to multi-year) variations related to migration of CO₂-rich magmatic fluids beneath the volcano. Accumulation chamber soil CO₂ flux surveys were also conducted in the four additional areas of diffuse CO₂ degassing on Mammoth Mountain in July–August 2013. Summing CO₂ emission rates for all five areas yielded a total for the mountain of 311 t d^{− 1}, which may suggest that emissions returned to 1998–2009 levels, following an increase from 2009 to 2011.