We explore, both experimentally and theoretically, the response of an elongated Bose-Einstein condensate to modulated interactions. We identify two distinct regimes differing in modulation frequency and modulation strength. Longitudinal surface waves are generated either resonantly or parametrically for modulation frequencies near the radial trap frequency or twice the trap frequency, respectively. The dispersion of these waves, the latter being a Faraday wave, is well reproduced by a mean-field theory that accounts for the 3D nature of the elongated condensate. In contrast, in the regime of lower modulation frequencies, we find that no clear resonances occur, but with an increased modulation strength, the condensate forms an irregular granulated distribution that is outside the scope of a mean-field approach. We find that the granulated condensate is characterized by large quantum fluctuations and correlations, which are well described with single-shot simulations obtained from wave functions computed by a beyond-mean-field theory at zero temperature, the multiconfigurational time-dependent Hartree for bosons method.