This paper presents a method to analyze and improve the set of equations constituting a rainfall-runoff model structure based on a combination of a data assimilation algorithm and polynomial updates to the state equations. The method, which we have called “Data Assimilation Informed model Structure Improvement” (DAISI) is generic, modular, and demonstrated with an application to the GR2M model and 201 catchments in South-East Australia. Our results show that the updated model generated with DAISI generally performed better for all metrics considered included KGE, NSE on log transform flow and flow duration curve bias. In addition, the modelled elasticity of runoff to rainfall is higher in the updated model, which suggests that the structural changes could have a significant impact on climate change simulations. Finally, the DAISI diagnostic identified a reduced number of update configurations in the GR2M structure with distinct regional patterns in three sub-regions of the modelling domain (Western Victoria, central region, and Northern New South Wales). These configurations correspond to specific polynomials of the state variables that could be used to improve equations in a revised model. Several potential improvements of DAISI are proposed including the use of additional observed variables such as actual evapotranspiration to better constrain the model internal fluxes.