We present ALMA observations of the dwarf starburst galaxy Henize 2-10 in combination with previous SMA CO observations to probe the molecular environments of natal super star clusters. These observations include the HCO$^+$(1-0), HCN(1-0), HNC(1-0), and CCH(1-0) molecular lines, as well as 88 GHz continuum with a spatial resolution of $1.7times 1.6$. After correcting for the contribution from free-free emission to the 88 GHz continuum flux density ($sim$ 60% of the 88 GHz emission), we derive a total gas mass for He~2-10 of $M_{gas} = 4-6times10^8$ M$_{odot}$, roughly 5-20% of the dynamical mass. Based on a principle component analysis, HCO$^+$ is found to be the best general tracer of molecular emission. The line widths and luminosities of the CO emission suggests that the molecular clouds could either be as small as $sim 8$ pc, or alternately have enhanced line widths. The CO emission and 88 GHz continuum are anti-correlated, suggesting that either the dust and molecular gas are not cospatial, which could reflect the 88 GHz continuum is dominated by free-free emission. The CO and CCH emission are also relatively anti-correlated, which is consistent with the CCH being photo-enhanced, and/or the CO being dissociated in the regions near the natal super star clusters. The molecular line ratios of regions containing the natal star clusters are different from the line ratios observed for regions elsewhere in the galaxy. In particular, the regions with thermal radio emission all have CO(2-1)/HCO$^+(1-0) < 16$, and the HCO$^+$/CO ratio appears to be correlated with the evolutionary stage of the clusters.
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