Given the fact that artificial intelligence tools such as neural network and fuzzy logic are capable of learning and inferencing from the past to capture the patterns that exist in the data, this study presents an intelligent method for the forecasting of water diffusion through carbon nanotubes where predictions are generated from neurofuzzy structures using molecular dynamics data. Therefore, this research was mainly focused on combining molecular dynamics with artificial intelligence methods in order to reduce the computational time of biomolecular and nanofluidic simulations. Two different artificial intelligence methods are applied for the time-dependent water diffusion forecasting: artificial neural network (ANN) and adaptive neuro-fuzzy inference systems (ANFISs). The effects of different sizes of training sample sets on forecasting performance of ANN and ANFIS are investigated as well. Four different evaluation methods are used to measure the performance and forecasting accuracy of these two methods. As a result, ANFIS presents the higher accuracy than neural network method based on the comparison of these different evaluation methods adopted in this research. The results reported in this research demonstrate that combining of molecular dynamics with artificial intelligence methods can be one of the most powerful and beneficial tools for prediction of important nanofluidic parameters.