Morphological and biochemical responses were assessed in an iceberg (GIL) and butterhead (GBL) lettuce (Lactuca sativa var. capitata) treated with commercially available soluble preparation of mycorrhizal fungi and beneficial soil bacteria (MT) grown in three irrigation treatments considered in greenhouse (continental Croatia, 2022): I100—control treatment (100% volumetric water content—VWC); I80—80% VWC, moderate drought and I60—60% VWC, severe drought), in two growing cycles. MT was applied during lettuce drought-sensitive stages, i.e., transplanting and heading. Study results show that MT improved lettuce growth-related traits, yet the results are genotype and growing-cycle dependent. The beneficial effect of MT was also noted for root length, weight, and diameter which confirms the mycorrhizal role in improving the plant water uptake. Both lettuce genotypes responded to water deficit by overproduction of MDA and proline content, whereby the response of tested variables was growing cycle and genotype-specific. Both genotypes in severe drought treatment (MT-I60) responded with higher MDA in the first growing cycle and lower MDA content in the second growing cycle. MT-I60 treatment reduced proline accumulation in GBH in both growing cycles, while increased accumulation in GIL during the second growing cycle. The responses of lettuce to MT are genotype-specific and shaped by environmental conditions.