Groundwater is a key resource for water supply in the Saguenay-Lac-Saint-Jean (SLSJ) region, Quebec. Growing pressures from climate variability, land-use change, and increasing water demand highlight the need for a groundwater sustainability plan. Developing such tools, however, raises a series of methodological and data-related challenges that are often underestimated. This contribution presents ongoing work focused on the construction of tools to support groundwater sustainability planning in the SLSJ region. The first objective aims to characterise the current (static) state of groundwater resources using indicators of sustainable development. Major challenges relate to the fragmented and uneven nature of groundwater data, both in space and time, which limits the direct estimation of indicators. In addition, characterising a “current” state implicitly assumes temporal stability, despite groundwater systems responding over multiple timescales to past and ongoing stresses. Despite these limitations, sustainability indicator based on recharge estimates and groundwater abstraction volumes provide a valuable initial assessment of the pressure exerted on the resource. However, estimation of the recharge is usually very difficult. Addressing these challenges requires methodologies that explicitly integrate hydrogeological knowledge, acknowledge scale and non-stationarity issues. The second objective focuses on representing groundwater dynamics through an integrated groundwater–agent-based modelling framework. Here, challenges arise from the scarcity of behavioural and socio-economic data needed for agent parameterisation, as well as from the conceptual and technical complexity of coupling agent-based models with physically based groundwater models. To manage this complexity, simplified model structures and hypothesis-driven representations are explored as intermediate steps.