Water flowrates and flow directions may change over time in the subsurface for a number of reasons. In fractured rocks flow takes place in channels within fractures. Solutes are carried by the advective flow. In addition, solutes may diffuse in and out of stagnant waters in the rock matrix and other stagnant water regions. Sorbing species may sorb on fracture surfaces and on the micropore surfaces in the rock matrix. We present a method by which solute particles can be traced in flowing water undergoing changes in flowrate and direction in a complex channel network where the solutes can also interact with the rock by diffusion in the rock matrix. The novelty of this paper is handling of diffusion in the rock matrix under transient flow conditions. The diffusive processes are stochastic and it is not possible to follow a particle deterministically. The method therefore utilises the properties of a probability distribution function for a tracer moving in a fracture where matrix diffusion is active. The method is incorporated in a three dimensional channel network model. Particle tracking is used to trace out a multitude of flowpaths, each of which consists of a large number of channels within fractures. Along each channel the aperture and velocity as well as the matrix sorption properties can vary. An efficient method is presented whereby a particle can be followed along the variable property flowpath. For stationary flow conditions and a network of channels with advective flow and matrix diffusion, a simple analytical solution for the residence time distribution along each pathway can be used. Only two parameter groups need to be integrated along each path. For transient flow conditions, a time stepping procedure that incorporates a stochastic Monte-Carlo like method to follow the particles along the paths when flow conditions change is used. The method is fast and an example is used for illustrative purposes. It is exemplified by a case where land rises due to glacial rebound. It is shown that the effects of changing flowrates and directions can be considerable and that the diffusive migration in the matrix can have a dominating effect on the results.