We extend the natural orbital impurity solver [PRB 90, 085102 (2014)] to finite temperatures within the dynamical mean field theory and apply it to calculate transport properties of correlated electrons. First, we benchmark our method against the exact diagonalization result for small clusters, finding that the natural orbital scheme works well not only for zero temperature but for low finite temperatures. The method yields smooth and sufficiently accurate spectra, which agree well with the results of the numerical renormalization group. Using the smooth spectra, we calculate the electric conductivity and Seebeck coefficient for the two-dimensional Hubbard model at low temperatures which are in the scope of many experiments and practical applications. These results demonstrate the usefulness of the natural orbital framework for obtaining the real frequency information within the dynamical mean field theory.