This paper focuses on the problem of quantifying the effects of model-structure uncertainty in the context of timeevolving dynamical systems. This is motivated by multi-model uncertainty in computer physics simulations: developers often make different modeling choices in numerical approximations and process simplifications, leading to different numerical codes that ostensibly represent the same underlying dynamics. We consider model-structure inference as a two-step methodology: the first step is to perform system identification on numerical codes for which it is possible to observe the full state; the second step is structural uncertainty quantification (UQ), in which the goal is to search candidate models "close" to the numerical code surrogates for those that best match a quantity-of-interest (QOI) from some empirical dataset. Specifically, we: (1) define a discrete, local representation of the structure of a partial differential equation, which we refer to as the "local dynamical operator" (LDO); (2) identify model structure non-intrusively from numerical code output; (3) non-intrusively construct a reduced order model (ROM) of the numerical model through POD-DEIM-Galerkin projection; (4) perturb the ROM dynamics to approximate the behavior of alternate model structures; and (5) apply Bayesian inference and energy conservation laws to calibrate a LDO to a given QOI. We demonstrate these techniques using the two-dimensional rotating shallow water (RSW) equations as an example system. operator (LDO), which is simply a functional relationship between spatially-local field values that approximates the discretized governing field dynamics at a spatial point. For example, if the governing equations are hyperbolic, then the LDO is a function that takes field values in a spatially-local neighborhood of a center point and outputs the field value at that center point, one time step forward in time. Note that there is an attractive consequence of our assumptions of locality and spatio-temporal invariance with respect to system identification: if we wish to infer a LDO from numerical/experimental data, access to the full global state vector is not strictly required. We may simply collect data from a subset of spatial points (together with the appropriate surrounding local neighborhoods). This is a notable advantage relative to a system identification technique that would require the full global state vector (e.g., POD).As all of the dynamics are encoded in the LDO, any structural uncertainties are as well. Furthermore, if we can design the LDO to be a weighted sum of different elementary functions of the local field values, then the relevant structural uncertainties manifest themselves as uncertainties in the values of the weights, which are simply parameters. This is a sketch of the process by which we convert structural uncertainties to parametric ones.Having formalized a means to parameterize model structure, all of the machinery of parametric uncertainty quantification (UQ) is available to study the structural uncert...