Ancient Hebrew scribes and Masoretes deliberately encoded interpretive traditions into biblical manuscripts through subtle textual modifications, revealing a sophisticated system of "Bible codes" distinct from modern letter-sequence theories. Unlike the debunked equidistant letter sequence phenomenon, these authentic encodings emerged through careful orthographic choices and vocalization patterns across manuscript traditions. Comparative textual analysis of variant spellings and masoretic vocalizations demonstrates how scribal schools modified letter sequences to embed midrashic readings. Notable examples include the expanded spelling of *mayim* (water) in Numbers 29's Sukkot passages, authenticating the water libation ceremony's biblical roots, and strategic variations in *tol'dot* (generations) that reflect theological concepts of completeness and deficiency. The double *yod* in *vayyitzer*, differentiating human from animal creation, encoded the dual inclination doctrine. The Masoretes later extended this practice through specific vocalization choices, as evidenced in their treatment of *Adonai* in Genesis 18:3 and punctuation of Isaiah 63:9. These systematic textual interventions served to establish authoritative readings and strengthen rabbinic theological positions against sectarian interpretations, revealing a historically grounded tradition of encoded biblical interpretation.