The ocean is a very complex medium with scales of motion that range from thousands of kilometers to the dissipation scales. Transport by ocean currents plays an important role in many practical applications ranging from climatic problems to coastal management and accident mitigation at sea. Understanding transport is challenging because of the chaotic nature of particle motion. In the last decade, new methods have been put forth to improve our understanding of transport. Powerful tools are provided by dynamical system theory, that allow the identification of the barriers to transport and their time variability for a given flow. A shortcoming of this approach, though, is that it is based on the assumption that the velocity field is known with good accuracy, which is not always the case in practical applications. Improving model performance in terms of transport can be addressed using another important methodology that has been recently developed, namely the assimilation of Lagrangian data provided by floating buoys. The two methodologies are technically different but in many ways complementary. In this paper, we review examples of applications of both methodologies performed by the authors in the last few years, considering flows at different scales and in various ocean basins. The results are among the very first examples of applications of the methodologies to the real ocean including testing with Lagrangian in-situ data. The results are discussed in the general framework of the extended fields related to these methodologies, pointing out to open questions and potential for improvements, with an outlook toward future strategies.