Size-based modelling approaches are an efficient way to analyse multi-species dynamics and responses to environmental perturbations including climate change, sedimentation, and fishing. Here, we present three multi-species size-structured models of New Zealand using the R package mizer: (i) Chatham Rise, (ii) Tasman Bay and Golden Bay, and (iii) the Poor Knights. Each has differing environmental conditions, involves multiple species and fitting to observational data, which will be described. We investigate the steady state properties of each, before perturbing the systems using historical measures of temperature and resource abundance available through the Fisheries and Marine Ecosystem Model Intercomparison Project (FishMIP) and other sources. Finally, future climate projections are used to investigate impacts on the ecosystem structure of each system. Issues raised during the study will be highlighted, with the respective solutions employed and practical suggestions offered for others undertaking climate studies using size-based models in the future.