documentclass{beamer}
usepackage[english]{babel}
usepackage[utf8x]{inputenc}
usepackage{tikz-cd}
usepackage{amsmath,amssymb,amsthm}

begin{document}

begin{equation*}
begin{tikzcd}
  text{The following lines are not aligned} arrow{d}
\
begin{aligned}
     &  Line 1\
     &  Line 2 text{(Not aligned at the beginning!)}
end{aligned}
end{tikzcd}
end{equation*}

end{document}