In 1989, Ponomaryov filled the place of academic Andrei Sakharov in the Congress of People's Deputies of the Soviet Union after he died suddenly from a heart attack.

Ponomaryov took part in the Coordination Council of Moscow Union of Electors and in the initiative group for the creation of the Civil Action Committee.

[1] In the autumn of 1991, he presided over the parliamentary commission for investigation of GKChP activities and the KGB’s role in the 1991 Soviet coup d'état attempt.

Also in 1997, Ponomaryov was one of the founders of the "Hotline" (Goriachaia liniia) and founded and is one of the most active members of the group Common Action (Obshchee deistvie).

In 2009, together with other Solidarnost activists, Roman Dobrokhotov, Oleg Kozlovsky, Aleksander Rykline, Sergey Davidis, Mikhail Schneider, Vladimir Milov, Garry Kasparov and Boris Nemtsov, Lev Ponomaryov took part in a series of individual pickets in front of Meschansky district court and held a slogan "Freedom to Mikhail Khodorkovsky and Platon Lebedev".

At the meeting of Russian and US Presidents on 1 April 2009, Barack Obama, according to his assistants, mentioned the attack against Ponomarev among the main US concerns about Russia.

Ponomaryov was sentenced to at least 25 days of detention in December 2018 in because of a Facebook post publicising an unauthorised rally that was to take place at Lubyanka square in Moscow on 28 October.

[3] On 30 January 2022, during the 2021–2022 Russo-Ukrainian crisis, Ponomaryov led a public declaration published in Echo of Moscow opposing the Russian threat to further invade Ukraine.

[4][5][6] On 20 February 2022, Ponomaryov and seven others, including Yuri Samodurov, held solitary street protests in Moscow against the Russian threat to attack Ukraine and were arrested.

[10] On 22 March 2012, Komsomolskaya Pravda published transcripts of a YouTube video, purporting to show Ponomaryov to be demanding money for civil organizations in the Russian Far East from an official working at the Embassy of Japan in Moscow, in return for promoting Japanese claims to the disputed Kuril Islands of Shikotan and Habomai.

The video also purports to show him saying that people like Boris Nemtsov, Mikhail Kasyanov and Vladimir Ryzhkov would go to blood[clarification needed] if allowed to handle it.