With the rejuvenated emphasis on nonpoint pollution under the Water Quality Act (WQA) of 1987, states seek ways to address nonpoint pollution sources in their states. States can use Clean Water State Revolving Funds (CWSRF) to address nonpoint needs; these funds are administered by state agencies, and funding decisions are typically made by agency personnel. While some states have aggressively funded nonpoint projects, other states have been much more reticent. Moreover, states have created different administrative structures to administer these funds. Does the nature of the structure impact the distribution of loans? Utilizing a dataset spanning state-level data from 1988 to 2016, we test a novel negative binomial cross-sectional time-series model employing the number of CWSRF loans directed to nonpoint project as the dependent variable. We find that states where water quality management is buried within a ‘mini-EPA’ agency are the least likely to allocate CWSRF loans for nonpoint source issues, whereas states with ‘super’ agencies or combined environmental/health agencies allocate a higher number of CWSRF loans to nonpoint source projects.