We present the first high-resolution sub-mm survey of both dust and gas for a large population of protoplanetary disks. Characterizing fundamental properties of protoplanetary disks on a statistical level is critical to understanding how disks evolve into the diverse exoplanet population. We use ALMA to survey 89 protoplanetary disks around stars with $M_{*}>0.1$ $M_{⊙}$ in the young ($∼$1-3 Myr), nearby ($∼$150-200 pc) Lupus complex. Our observations cover the 890 $μ$m continuum and the $^{13}$CO and C$^{18}$O 3-2 lines. We use the sub-mm continuum to constrain $M_{\rm dust}$ to a few Martian masses (0.2-0.4 $M_{⊕}$) and the CO isotopologue lines to constrain $M_{\rm gas}$ to roughly a Jupiter mass (assuming ISM-like $\rm {[CO]/[H_2]}$ abundance). Of 89 sources, we detect 62 in the continuum, 36 in $^{13}$CO, and 11 in C$^{18}$O at $>3σ$ significance. Several new "transition disks" are found with relatively bright continuum and CO isotopologue emission. Stacking the individually undetected sources limits their average dust mass to $\lesssim6$ Lunar masses (0.03 $M_{⊕}$), indicating rapid evolution once disk clearing begins. We find a positive but non-linear correlation between $M_{\rm dust}$ and $M_{*}$, and also demonstrate for the first time a tentative positive correlation between $M_{\rm gas}$ and $M_{*}$. The mean dust mass in Lupus is 3$\times$ higher than in Upper Sco, while the dust mass distributions in Lupus and Taurus are statistically indistinguishable from each other. Most detected disks have $M_{\rm gas}\lesssim1$ $M_{\rm Jup}$ and gas-to-dust ratios $<100$ when using our parameterized model framework; if confirmed, the inferred rapid gas depletion indicates that planet formation is largely complete by a few Myr, and may also explain the unexpected prevalence of super-Earths in the exoplanet population.