Heherson T. Alvarez was elected representative of the 4th District of Isabela in May 1998 under the Lakas-NUCD-UMDP party which he then served as Secretary General. He served one term as congressman at the House of Representatives during the 11th Congress, from 1998 to March 2001.
A leading member of the opposition and the minority block at that time, he is best remembered as the principal initiator of the impeachment complaint filed against former President Joseph Estrada at the time when everybody else thought the idea was almost a "fantasy" and no one supported the complaint.
Against all odds, the impeachment complaint gathered steam and began to snowball after more evidences surfaced, convincing his colleagues that there was probable cause to file the complaint against former President Estrada.
The impeachment complaint paved the way for EDSA II. In recognition of Alvarez' s effort the People Power Commission gave him the EDSA People Power Freedom Award.
As a member of the House of Representatives in 1999, he led the fight against the proliferation of pornographic images in the movie and television industry, together with a multi-sectoral group of religious and civil society members.
This culminated in the "Jericho March" of thousands of concerned Filipinos at the Philippine Senate grounds, resulting to a Senate inquiry that led to a renewed effort from the local movie industry to police itself.
Also in 1999, Alvarez spearheaded a move to oppose the plan of the Marcos family to bury the late President Ferdinand E. Marcos at the Libingan ng mga Bayani in Fort Bonifacio in Makati City.
The massive rally Alvarez led at the Don Chino Roces Bridge, attended by religious leaders, the youth, former President Aquino and other political luminaries who opposed Martial Law, prompted former President Estrada to finally cave in and keep the remains of the late dictator in a refrigerated crypt in Ilocos Norte.
In March 2001, recognizing his steadfast commitment to good governance and his passion for the protection of the environment through sustainable development, President Arroyo appointed him as Secretary of the Department of Environment and Natural Resources (DENR).
He continued to be the leading voice on the environment in the House of Representatives where he was responsible for the enactment of the following laws:
• Northern Sierra Madre Natural Park Act (RA 9215), protecting the country's last remaining virgin forests and pristine waters, including the many plants and animals that thrive in it such as the Philippine Eagle, the dugong, and many others.
• Solid Waste Management Act (RA 9003), the first measure signed into law by President Gloria Macapagal Arroyo, which promotes ecological waste management and creates necessary institutions for its implementation.
• Clean Air Act (RA 8479), setting standards for ambient air and emissions from all air pollution sources and strengthened the government structure for implementation and enforcement.
As congressman, he also filed the following comprehensive package of proposed measures in the 11th Congress that would address the entirety of environmental degradation:
• Smoking Ban Act
• Clean Water Act
• Total Commercial Log Ban Act
• Land Use Act
• Community-Based Forest Management Act
• National Environmental Management Authority (NEMA) Act
• Wildlife Resources Conservation Act
• Revision of the Environment Code
• Biomedical Waste Control Act
• New Pollution Control Law
• Mangroves Protection and Conservation Act
• Creation of Special Environmental Courts
• Indigenous Oil and Gas Act
• Energy Conservation Act
• Geothermal Act
His important measures approved on Third Reading in the 11th Congress were:
• Omnibus Electric Industry Restructuring Act
• Anti-Racketeering-Influenced and Corrupt Organizations Act
• Anti-Trafficking in Filipino Women Act