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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 Kling‐Gupta Efficiency, NSE on log transform flow and flow duration curve bias. In addition, the elasticity of modeled 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 modeling 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 internal model fluxes. Plain Language Summary: This paper presents a data‐driven method to improve rainfall‐runoff models used to generate future water resources scenario in climate change studies. The method, which we have called "Data Assimilation Informed model Structure Improvement" (DAISI) is generic, modular, and demonstrated with an application to monthly streamflow simulations over a large data set of catchments in South‐East Australia. Our results show that DAISI improves model performance for a wide range of metrics and increases the sensitivity of the model to climate inputs, which is critical in climate change scenarios. Finally, the improvements identified by DAISI take a simple mathematical form with distinct regional patterns in three sub‐regions of the study domain (Western Victoria, central region, and Northern New South Wales). Several improvements of DAISI are discussed including the inclusion of additional observed variables such as evapotranspiration to better constrain model simulations. Key Points: Data Assimilation Informed model Structure Improvement method diagnoses hydrological model structures by combining data assimilation with a polynomial update of state equationsThe method was applied to the GR2M rainfall‐runoff model with significantly improved streamflow simulations in 201 Australian catchmentsThe method identified updates to state equations with marked regional characteristics that could guide future improvement of GR2M [ABSTRACT FROM AUTHOR]