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Improving nitrogen (N) fertilizer management in agricultural systems is critical to meeting environmental goals while maintaining economically viable and productive food systems. This paper applies a farm systems framework to analyze how adoption of N management practices is related to different farming operation characteristics and the extent to which fertilizer, soil and irrigation practices are related to each other. We develop a multivariate probit regression model to analyze the interdependency of these adoption behaviors from 966 farmers across three watersheds and diverse cropping systems in the Central Valley of California. Our analysis demonstrates that farmers adopt varying combinations or portfolios of practices, with the most common portfolio featuring a core set of fertilizer-focused practices. Irrigation infrastructure is an especially important farm operation characteristic for encouraging adoption of innovative practice portfolios that integrate water and fertilizer management. These findings highlight the ability for a farm systems approach to improve our understanding of farmer decision-making across diverse agricultural landscapes.