In this work we investigate how event-by-event hydrodynamics fluctuations affect the nuclear suppression factor and elliptic flow of heavy flavor mesons and non-photonic electrons. We use a 2D+1 Lagrangian ideal hydrodynamic code on an event-by-event basis in order to compute local temperature and flow profiles. Using a strong coupling inspired energy loss parametrization on top of the evolving space-time energy density distributions we are able to propagate the heavy quarks inside the medium until the freeze-out temperature is reached and a Pythia modeling of hadronization takes place. The resulting D$^0$ and heavy-flavor electron yield is compared with recent experimental data for $R_text{AA}$ and $v_2$ from the STAR and Phenix collaborations. In addition we present preditions for the higher order Fourier harmonic coefficients $v_3(p_T)$ of heavy-flavor electrons at RHICs $sqrt{S_text{NN}} = 200$ GeV collisions.