Healthy Fisheries through Better Science Act

Healthy Fisheries through Better Science Act - Amends the Magnuson-Stevens Fishery Conservation and Management Act to require the Secretary of Commerce to develop and publish at least triennially in the Federal Register (on the same schedule as the fisheries research strategic plan) a plan to conduct stock assessments for all stocks of fish for which a fishery management plan is in effect.

Defines "stock assessment" as an evaluation of the past, present, and future status of a stock of fish, including: (1) a range of life history characteristics, including the stock's geographical boundaries, age, growth, natural mortality, sexual maturity and reproduction, feeding habits, and habitat preferences; and (2) fishing for the stock.

Requires the plan to: (1) establish schedules for conducting initial stock assessments and updating previously conducted assessments; and (2) identify data and analysis, especially concerning recreational fishing, that would reduce uncertainty in and improve the accuracy of future stock assessments, including whether such data and analysis could be provided by nongovernmental sources, such as fishermen, fishing communities, universities, and research institutions. Provides for waivers of stock assessment requirements when the Secretary determines that the assessment is not necessary and justifies such determination in the Federal Register notice.

Directs the Secretary to develop and publish in the Federal Register guidelines to incorporate data, analysis, and stock assessments from nongovernmental sources into fisheries management decisions and to establish a registry of information providers. Requires the Secretary and Regional Fishery Management Councils to use such information as the best scientific information available in fisheries management decisions, unless otherwise determined by the science and statistical committee of such Councils.

Directs the Secretary to report to Congress regarding each fishery governed by a fishery management plan to: (1) identify the goals and methods of the applicable programs governing monitoring and enforcement of fishing subject to such plan; (2) certify which methods are most cost-effective; and (3) explain why such most-cost-effective methods are not required, if applicable.

Prohibits the Secretary from collecting certain fishing permit fees and North Pacific Council fisheries research plan implementation fees before identifying the costs that will be recovered by such fee.