Walter Araujo, head of the Supreme Elections Council, said he was satisfied with the "good rythm" of the voting, despite logistical problems that kept many voting centers from opening on time early in the day.
"The inflow is massive in the voting centers, people are arriving, the centers are full, people are walking in with families," Araujo said.
Many voting centers opened over an hour late due to the lack of indelible ink, paper and pens, and other problems, forcing voters into lengthy queues. Some instead returned home or went on to jobs.
The polls otherwise went off mostly without incident, with police reporting they had detained about 10 people after five hours of voting, some for "election fraud".
According to opinion polls, the issues most driving voters include unemployment and a high rate of murders connected to delinquency.
About 3.8 million Salvadorans are voting for 84 deputies in the assembly and for local municipal governments in 262 cities and towns.
The battle for many positions set the centre-right National Republican Alliance of President Elias Antonio Saca Gonzalez against the left wing Farabundo Marti National Liberation Front (FMLN).
FMLN was the main rebel group during El Salvador's 1980s civil war, which left 75,000 dead and another 6,000 missing. FMLN became a legal political party in a 1992 peace deal.
The voting was scheduled to close at 5:00pm local time (2300 GMT), and the electoral council said it hoped to have the first results ready four hours later.