Our understanding of complex marine ecosystem dynamics is often hindered by significant uncertainties and issues of representativeness associated with models and observations. Both observations and models provide a limited view of real-world complexities depending on what is specifically measured or simulated. When used together, they provide the ability to gain a broader understanding of important ecological processes. How to properly integrate models and observations while utilizing the advantages of both approaches remains a challenge. In this paper, we draw attention to commonly overlooked limitations of both observations and models, and use examples to illustrate potential strategies to mitigate bias, properly interpret results, and help improve both models and observations. We emphasize that proper validation of all data sources (models and observations) is necessary in all marine ecosystem studies, with a careful assessment of the spatio-temporal scales that the data represent.