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A critical question in relation to inter-agency coordination is not only whether, but how, to coordinate. This question is particularly salient when agencies are subject to a top-down mandate. While inter-agency coordination can provide multiple benefits, agencies frequently have concerns about the potential risks of coordination. Differing coordination mechanisms may reduce or exacerbate those concerns. Depending on their coordination concerns, agencies will be inclined to favor certain mechanisms over others. Examination of the implementation of California’s Sustainable Groundwater Management Act, which mandates local agency coordination, indicates that coordination mechanism selection is influenced by which combination of concerns agencies hold, with autonomy considerations taking priority over other concerns. These findings suggest opportunities to improve the explanatory power of theories of inter-agency coordination by incorporating potential hierarchies of concerns, their distribution across the multiple agencies tasked with coordinating, and configurational effects. To this end, we propose a contingency theory of agency concerns and coordination mechanism choice under a mandate to coordinate.