Using numerical modeling we study emergence of structure and structure-related nonlinear conduction properties in the self-assembled nanoparticle films. Particularly, we show how different nanoparticle networks emerge within assembly processes with molecular bio-recognition binding. We then simulate the charge transport under voltage bias via single-electron tunnelings through the junctions between nanoparticles on such type of networks. We show how the regular nanoparticle array and topologically inhomogeneous nanonetworks affect the charge transport. We find long-range correlations in the time series of charge fluctuation at individual nanoparticles and of flow along the junctions within the network. These correlations explain the occurrence of a large nonlinearity in the simulated and experimentally measured current-voltage characteristics and non-Gaussian fluctuations of the current at the electrode.