Among one of the key challenges in dairy production is the management of manure in a way that is beneficial for agricultural production, with minimal environmental and public health impacts. Manure management systems (MMS)-the entire system of handling, storage, and application of manure-are diverse in countries with developed dairy industries such as the United States, enabled by a number of different technologies. The ways in which dairy farmers manage manure is driven by varying tradeoffs, including economic, social, and environmental; however, existing research has not examined the relationships between components of MMS. Here we use data from the National Animal Health Monitoring System's Dairy 2014 study to explore the ways in which manure handling, storage, and application are related, using a series of logistic regression models and network associations. We found significant associations between how manure is handled, stored, and applied, especially driven by the consistency of manure. For solid manure, we found highly heterogeneous systems, where farmers may have a suite of alternative manure management strategies available to them, and substitution is viable. Conversely, farms using liquid manure systems have very few substitutes in their MMS, suggesting greater investment in certain infrastructures, which are not easily changed. Such findings have important implications for shifting farmers towards management practices with minimal environmental and public health impacts, demonstrating that not all farm systems are easily changed. We highlight these results in light of current policies, which may not fully capture the relationships across the MMS, and suggest that greater financing may be necessary to shift MMS on some farms. Furthermore, we suggest that different MMS have varying tradeoffs across environmental, social, and economic aspects, which demonstrates that MMS are highly individualized to a given farm's goals and priorities.