Organizers of the march released a statement saying the Istanbul governorship was not allowing the procession, citing the Muslim holy month of Ramadan.
Paradegoers continued to celebrate in the side streets, as riot police chased other attendees from arteries of Istanbul's main commercial district of Taksim.
One video shows a gay pride attendee being swept off his feet with the force of a water cannon.
Activists say they weren't just targeted because of their sexual orientation or fight for equality, but because Turkey's government wants to silence all minorities and anyone officials perceives as a threat to the conservative ruling Justice and Development Party.
Led by President Recep Tayyip Erdogan, the ruling party failed to secure enough votes
for a single-party rule in June.
CNN spoke to many sources who felt that the crackdown on Sunday's march was an attempt to appeal to Erdogan's conservative base.
"This is happening after the elections because they realize the power of the LGBTI movement," said transgender activist Ruzgar Buski. "Erdogan's government has lost their power and they know the LGBTI community stands with other minorities."
"We call on the Istanbul Governor Vasip Sahin to adhere to the Constitution of the Republic of Turkey, to immediately cease attacks and to make a public statement," said a statement from the volunteer group LGBTI News Turkey
Echoing a chant made famous in Western gay rights parades and events -- "We're here, we're queer, get used to it!" -- it said in capital letters, "WE ARE HERE, GET USED TO IT, WE ARE NOT LEAVING."
The gay, lesbian, bisexual, transgender and intersex community was instrumental in supporting the Gezi Park protests
that took place in 2013 against the ruling party.
On Sunday, a woman shouted, "This is not a crime, we are LGBT! We are not a crime! Come on, why you are doing this?"
A man approached her and yelled, "Shut up and go away!" He told CNN that he did not like gay people and they were causing problems in Turkey, and then stressed that the country is Muslim and, to him, being Muslim and gay were in conflict.
The clashes with police came after Friday's ruling by the U.S. Supreme Court in support of same-sex marriage, which LGBTI activists in Turkey celebrated.
Gay, trans and intersex people in Turkey say they aren't at the stage where they could imagine that kind of equality in their country.
"We are at the stage of 'Please don't kill us,'" said Sevval Kilic, a transgender activist who helped organize the pride parade. "We don't discuss equal marriage or employment rights or whatever. We are just demanding our basic human rights."
Sunday's clashes won't set that goal back, Kilic said. "It will make us stronger."