The interface between fluid flow and wall surfaces, known as the near-wall region, plays a critical role in biological systems due to the exchanges between the wall tissue and fluid flow. Appreciation of the fluid dynamics and interaction between the flow and wall in this region is vital for numerous medical purposes, such as improving the diagnosis and treatment of diseases related to biological conduits and optimising particle transport drug delivery in the respiratory and cardiovascular systems. The focus of this PhD thesis is to investigate physiological fluid dynamics, particularly in the cardiovascular and respiratory systems, with a specific emphasis on fluid flow and particle dynamics in the near-wall region. With considerations of the primary source of data being non-invasive medical images, a versatile physically motivated image processing method is first developed. Subsequently a variety of mathematical techniques, including harmonic maps, polynomial expansion of near-wall flow, and three-dimensional mapping of the flow field, are employed. A mapping framework is introduced to improve the analysis of the near-wall flow in the computational domain by transferring the flow field into a simplified auxiliary space and defining it through analytical expressions. This provides a clearer visualization and closer examination of the fluid mechanics close to the wall, and enables the modelling of particle dynamics in the isolated mapped region exclusively. Furthermore, a substantial part of the thesis focuses on the development of some physically motivated fluid mechanics measures that can describe particle dynamics in the near-wall region. These measures relate particle deposition to local flow properties and can be utilised to predict deposition on the wall. Finally, the tools and techniques developed in the thesis are further applied to the human upper respiratory tract as a complex wall geometry in biological conduits, and their applications are discussed.