This dissertation provides a theoretical effective description of a special class of hadronic meson states with charm and bottom quark content and their associated phenomenology. The considered states are difficult to be accommodated in CQMs and are candidates to be interpreted as meson molecules. This relies on the assumption that their main properties can be described by means of an effective low energy interaction of two more fundamental mesons. We have paid special attention to the relevant symmetries of QCD and two-body unitarity to construct the low energy effective meson-meson interactions. We have investigated the predictions of the Next-to-Leading Order (NLO) Unitary Heavy Meson Chiral Perturbation Theory (UHMchiPT) scheme in the strangeness-isospin (S,I)=(0,1/2) sector, where so far the single D*0(2400) has been reported in experiments. We have found that in the energy region of the D*0(2400) there are in fact two-poles in the scattering amplitudes. With all the parameters previously fixed, we have predicted the energy levels for the coupled-channel system in finite volumes, finding that they agree remarkably well with a recent lattice QCD (LQCD) calculation on the same system. The NLO UHMχPT amplitudes solve various puzzles in the charm-meson spectrum if the D*s0(2317) and Ds1(2460) states owe their existence to the nonperturbative dynamics of Goldstone-boson scattering off D(s) and D*(s) mesons. We have demonstrated for the first time that this mechanism is strongly supported by the high quality data on the B -> D pi pi reaction provided by the LHCb experiment. Besides, we have used the NLO UHMχPT scheme as input in a dispersive description of the available data on scalar hadronic form factors of weak semileptonic decays of D(s) and B(s) mesons into a Goldstone boson. We have also proposed a new parametrization of hadronic form factors in semileptonic B->D decays. Using the most recent LQCD data on the Ds0(2317) and Ds1(2460) resonances and their bottom siblings, we have incorporated the interplay of constituent quark model states in the D(*)K and B(*)K S-wave meson-meson interaction. In this way, we have concluded that these states have a predominantly molecular structure. In order to further learn about the nature of the D*s0(2317), we have proposed measuring the Bc decay into J/psi KD. On the other hand, we have investigated the signatures produced by the Zc(3900) resonance in LQCD simulations. Finally, we have studied the ρ/ω and B(*) S-wave scattering, and found evidence of three bound states with J=0,1,2. The results obtained in this thesis reinforce the interpretation that the hadron spectrum should not be viewed as a collection of quark-model states. Instead, it should be regarded as a manifestation of complex dynamics, leading to an intricate and diverse pattern of states that can only be understood by a joint effort from experiment, LQCD and phenomenology.