**Abstract** : This HdR (“Habilitation à Diriger des Recherches) thesis is about complex fluids and complex flows applied to subsurface environments. The term “complex fluid” is rather standard and denotes fluids that consist of a mixture of two phases, solid-liquid, solid-gas or liquid-liquid. In this case I consider suspensions of colloidal particles in a liquid; their self-organization resulting from their interactions in-between them and with the liquid (sections 4.3.3 and 4.3.4), or from an external excitation (section 4.3.5), have a strong influence on the mechanical properties of the mixture and its flow. The term “complex flow” is to my knowledge no standard term. Here I mean by that a flow with a complex velocity field, in particular a wide distribution of velocities associated with strong spatial heterogeneities of the velocity field. As most of my work applies to subsurface processes, the Reynolds numbers involved are small, so that the flow field complexity can only result from the association of a geometric complexity of the flow boundary conditions and of small typical dimensions of the channels available for flow. It is the case when one considers the flow of a liquid in the pore space of a porous medium of even simple geometry (such as a bead pack), or inside a geological fracture. But it won’t be the case as soon as one has averaged local flow properties over a representative elementary volume (REL) to work at the Darcy scale. This means that most of my work involving what I call complex flows has considered flow, transport and reaction at the pore scale or at the scale of a fracture. The flow field complexity at these small scales has consequences at larger scales, be it at the fracture scale on a fracture’s transmissivity ( section 4.1.2), on the Darcys-scale relationship between pressure drop and saturation during unstable unsaturated flows (section 4.1.3), on the mass of product resulting from the reaction of two solutes transported by the flow (section 4.2.3), on the transit time of a solute transported by an unsaturated flow (section 4.2.4), on the efficiency of mixing in a three-dimensional porous medium (section 4.2.6), on the efficiency of a foam-based soil remediation process (section 4.1.4), or on the Darcy-scale measurement of an unsaturated medium’s electrical conductivity (section 6.4). One characteristics of my research work, for someone whose objects of interest belong to the subsurface, is therefore that I do Fluid Mechanics (in a broad sense) at scales that most hydrogeologists would rate between incredibly small (the nm) and very small (the m). The other characteristics is that most of my work relies on laboratory experiments. For these experiments my approach has always been to build analogue models of a geological object, in order to gain as complete a characterization of the investigated system as possible. In this thesis I shall mainly discuss analog models for two-dimensional porous media, in which we can measure both the spatial distribution of the various solid and fluid phases, the velocity field of liquids, and the concentration field of transported solutes or of solutes resulting from an in situ reaction. Using transparent setups allows the use of optical methods to measure those quantities, even in three dimensions (section 4.2.6). The motivation for this approach is to be able to obtain results as quantitative as possible, if possible with a quantitative theoretical explanation/predictions of the measurements. This perhaps betrays a Physicist’s background, but on the other hand I am very much aware of the necessity (and difficulty !) of choosing a suitable compromise between sufficient relevance to the real world object and capacity to infer quantitative findings. In particular, the analogue systems that I develop incorporate some level of disorder, if possible. This means that those systems, as natural systems, feature large fluctuations, which triggers the need for averaging, statistical analyses/models, upscaling schemes, and such. The document contains a curriculum vitae, a complete list of publications (articles and conference abstracts), a summary of my research activities between 2003 and 2015, a short description of my teaching and editorial activities, a presentation of the prospects for my future research, and a short conclusion. Given the variety of the topics addressed, the environmental context is presented per topic within the sections devoted to the summary of past research and when necessary to the research prospects, rather than inside a general introduction