Many political ecology debates hinge on the roles and outcomes of resource user regulation versus those arising from governance rules. Because of the difficulties of empirically testing theories of resource regulation, we evaluated the alternatives using a simulation modeling approach developed for East African coral reef fisheries where four scenarios of fisheries regulation on fish catch rates and resource ecology were evaluated. These scenarios were (1) a control simulation where fishing practices were held constant, (2) fishing that gradually incorporates fishers’ self-reported behavioral responses to declining resources, (3) rapid change where illegal gears were not allowed and effort was equally partitioned among the legal gears, and (4) gradual change where legal gears or exiting were adopted as yields decline. The model indicates that at moderate fishing effort (5 fishers/km2), the gradual behavioral change scenarios two and four produced the highest per fisher yields and maintained the highest fish biomass compared to the other two strict-control options. At high fisher numbers (10 fishers/km2), the rapid ban of illegal gear in scenario 3 had more similar ecological outcomes to gradual behavioral response scenarios 2 and 4. The model assumed no changes in behavior coming from outside the system or over longer periods of time that could potentially undermine or change the stated behavioral responses. The simulations show the difficulty of developing resource use regulations because of the complex interactions between numbers of fishers, behavioral responses, management decisions, and feedbacks to the resource. Nevertheless, the simulations indicate that at moderate fisher densities, governance strategies that allow resource users to respond to changing resources can produce better yield and resource outcomes than rigid control. Ecosystem models that do not incorporate fisher’s behavioral choices may overestimate their detrimental impacts.