Freshwater fisheries provide human benefits (e.g., food, recreation) but are increasingly threatened by climate change, invasive species, and other stressors. Our purpose was to survey fisheries administrators from state fisheries agencies and Agricultural Experiment Stations (AESs) about their perceptions of, and resource investment toward threats to freshwater fisheries in the United States. Our rationale for studying these two types of fisheries administrators simultaneously was to inform state fisheries professionals about the fisheries relevance of AESs, elevate the profile of fisheries within AESs, and promote mutually beneficial state agency–AES partnerships. Survey respondents generally agreed that recreational, socioeconomic, and ecological services of fisheries were more important than nutritional and commercial benefits. The greatest perceived fisheries threats were water quality/quantity impairment, land‐use change, and invasive species—but, interestingly, not climate change. State fisheries agencies invested more personnel and finances into issues rated as less important but more controllable (e.g., fish production, habitat management) than issues rated as more important but larger in scale and more difficult to control (e.g., water quality/quantity, invasive species). Our research underscores the importance of ensuring that state agencies can address long‐term, socio‐ecologically critical management issues (e.g., climate change) amid budgetary constraints. We call for state agencies to collaborate with new partners (e.g., AESs) to mitigate fisheries threats by expanding fisheries management to more fully encompass terrestrial and human systems; promoting receptiveness to novel research/management ideas; actively predicting, monitoring, and planning for future stressors; and enhancing fisheries social‐ecological resilience.